Starting phenix.real_space_refine on Fri Sep 11 11:58:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w6u_65704/09_2026/9w6u_65704.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w6u_65704/09_2026/9w6u_65704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w6u_65704/09_2026/9w6u_65704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w6u_65704/09_2026/9w6u_65704.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w6u_65704/09_2026/9w6u_65704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w6u_65704/09_2026/9w6u_65704.map" } resolution = 2.81 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= -0.002 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 5612 2.51 5 N 1487 2.21 5 O 1777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8908 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2188 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 256} Chain breaks: 1 Chain: "B" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 208} Chain: "C" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1583 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 14, 'TRANS': 198} Chain: "D" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1634 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 199} Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1721 Classifications: {'peptide': 230} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 216} Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 1.94, per 1000 atoms: 0.22 Number of scatterers: 8908 At special positions: 0 Unit cell: (72.98, 115.7, 157.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1777 8.00 N 1487 7.00 C 5612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 203 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " distance=2.04 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 213 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 301 " - " ASN A 122 " " NAG A 302 " - " ASN A 165 " " NAG A 303 " - " ASN A 234 " " NAG A 304 " - " ASN A 282 " " NAG A 305 " - " ASN A 17 " " NAG A 306 " - " ASN A 61 " " NAG A 307 " - " ASN A 74 " " NAG A 308 " - " ASN A 149 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 313.4 milliseconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 25 sheets defined 6.9% alpha, 43.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.210A pdb=" N THR B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 193 through 199 Processing helix chain 'C' and resid 25 through 32 removed outlier: 4.161A pdb=" N TYR C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.905A pdb=" N GLU C 85 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 129 Processing helix chain 'C' and resid 183 through 190 removed outlier: 3.528A pdb=" N HIS C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 183 through 189 removed outlier: 3.778A pdb=" N HIS D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.591A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 151 removed outlier: 3.611A pdb=" N GLY E 151 " --> pdb=" O SER E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.638A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.041A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 79 removed outlier: 3.524A pdb=" N HIS A 69 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP E 102 " --> pdb=" O ARG E 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.960A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER A 112 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N PHE A 135 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR A 114 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE A 133 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 11.224A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AA9, first strand: chain 'B' and resid 127 through 131 removed outlier: 3.887A pdb=" N GLY B 146 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP B 151 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TYR B 183 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 157 through 161 Processing sheet with id=AB2, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.179A pdb=" N GLN C 39 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU C 48 " --> pdb=" O GLN C 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.820A pdb=" N SER C 92 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL C 98 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 18 through 22 Processing sheet with id=AB5, first strand: chain 'C' and resid 116 through 120 removed outlier: 3.972A pdb=" N LEU C 134 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU C 180 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS C 136 " --> pdb=" O SER C 178 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 147 through 150 Processing sheet with id=AB7, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.597A pdb=" N GLU D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.558A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.603A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.077A pdb=" N GLY E 10 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.077A pdb=" N GLY E 10 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL E 119 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 137 through 141 removed outlier: 6.120A pdb=" N TYR E 193 " --> pdb=" O ASP E 161 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 137 through 141 removed outlier: 6.120A pdb=" N TYR E 193 " --> pdb=" O ASP E 161 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 167 through 171 removed outlier: 4.410A pdb=" N TYR E 211 " --> pdb=" O VAL E 228 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 882 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2823 1.34 - 1.46: 2258 1.46 - 1.58: 4008 1.58 - 1.70: 0 1.70 - 1.83: 40 Bond restraints: 9129 Sorted by residual: bond pdb=" CA PHE E 139 " pdb=" C PHE E 139 " ideal model delta sigma weight residual 1.520 1.541 -0.021 9.90e-03 1.02e+04 4.37e+00 bond pdb=" C1 NAG A 308 " pdb=" O5 NAG A 308 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" C1 NAG A 301 " pdb=" O5 NAG A 301 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" C1 NAG A 302 " pdb=" O5 NAG A 302 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C1 NAG A 303 " pdb=" O5 NAG A 303 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 ... (remaining 9124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 12242 2.36 - 4.73: 166 4.73 - 7.09: 19 7.09 - 9.45: 5 9.45 - 11.81: 1 Bond angle restraints: 12433 Sorted by residual: angle pdb=" N PRO E 140 " pdb=" CA PRO E 140 " pdb=" C PRO E 140 " ideal model delta sigma weight residual 112.47 121.49 -9.02 2.06e+00 2.36e-01 1.92e+01 angle pdb=" C ASN A 87 " pdb=" CA ASN A 87 " pdb=" CB ASN A 87 " ideal model delta sigma weight residual 116.34 110.59 5.75 1.40e+00 5.10e-01 1.69e+01 angle pdb=" CB MET B 48 " pdb=" CG MET B 48 " pdb=" SD MET B 48 " ideal model delta sigma weight residual 112.70 124.51 -11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" C ASN A 164 " pdb=" N ASN A 165 " pdb=" CA ASN A 165 " ideal model delta sigma weight residual 121.54 127.70 -6.16 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C LEU E 141 " pdb=" N ALA E 142 " pdb=" CA ALA E 142 " ideal model delta sigma weight residual 120.97 129.93 -8.96 2.84e+00 1.24e-01 9.96e+00 ... (remaining 12428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4760 17.98 - 35.96: 564 35.96 - 53.94: 165 53.94 - 71.93: 40 71.93 - 89.91: 9 Dihedral angle restraints: 5538 sinusoidal: 2212 harmonic: 3326 Sorted by residual: dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 38.73 54.27 1 1.00e+01 1.00e-02 3.99e+01 dihedral pdb=" CB CYS D 134 " pdb=" SG CYS D 134 " pdb=" SG CYS D 194 " pdb=" CB CYS D 194 " ideal model delta sinusoidal sigma weight residual -86.00 -126.59 40.59 1 1.00e+01 1.00e-02 2.31e+01 dihedral pdb=" CA ILE E 113 " pdb=" C ILE E 113 " pdb=" N THR E 114 " pdb=" CA THR E 114 " ideal model delta harmonic sigma weight residual 180.00 160.61 19.39 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 5535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1097 0.047 - 0.095: 219 0.095 - 0.142: 91 0.142 - 0.189: 1 0.189 - 0.237: 5 Chirality restraints: 1413 Sorted by residual: chirality pdb=" CA ASN A 165 " pdb=" N ASN A 165 " pdb=" C ASN A 165 " pdb=" CB ASN A 165 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CG LEU E 141 " pdb=" CB LEU E 141 " pdb=" CD1 LEU E 141 " pdb=" CD2 LEU E 141 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA PRO E 140 " pdb=" N PRO E 140 " pdb=" C PRO E 140 " pdb=" CB PRO E 140 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1410 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 41 " -0.044 5.00e-02 4.00e+02 6.66e-02 7.10e+00 pdb=" N PRO C 42 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 42 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 42 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 208 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.73e+00 pdb=" N PRO A 209 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 209 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 209 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 191 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO B 192 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 192 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 192 " -0.021 5.00e-02 4.00e+02 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 888 2.75 - 3.29: 7757 3.29 - 3.83: 13456 3.83 - 4.36: 15205 4.36 - 4.90: 28310 Nonbonded interactions: 65616 Sorted by model distance: nonbonded pdb=" OG1 THR B 28 " pdb=" OE2 GLU B 31 " model vdw 2.213 3.040 nonbonded pdb=" OG SER B 134 " pdb=" OG SER B 137 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.235 3.040 nonbonded pdb=" O SER A 112 " pdb=" OG SER A 112 " model vdw 2.262 3.040 nonbonded pdb=" O SER B 85 " pdb=" OG SER B 85 " model vdw 2.265 3.040 ... (remaining 65611 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=0.00 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: 3.340 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 8.670 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.003 0.040 9146 Z= 0.161 Angle : 0.697 11.814 12475 Z= 0.367 Chirality : 0.046 0.237 1413 Planarity : 0.005 0.067 1589 Dihedral : 17.222 89.907 3381 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.13 % Favored : 95.79 % Rotamer: Outliers : 3.33 % Allowed : 29.97 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.37 (0.25), residues: 1139 helix: 1.14 (0.78), residues: 53 sheet: 1.38 (0.24), residues: 484 loop : -0.84 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 44 TYR 0.010 0.001 TYR E 162 PHE 0.013 0.001 PHE D 209 TRP 0.012 0.001 TRP B 47 HIS 0.006 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 ( 9129) covalent geometry : angle 0.68706 / 0.36 (12433) SS BOND : bond 0.00636 / 0.30 ( 9) SS BOND : angle 1.46083 / 0.94 ( 18) hydrogen bonds : bond 0.12329 / 7.42 ( 322) hydrogen bonds : angle 5.94408 / 4.23 ( 882) link_NAG-ASN : bond 0.00290 / 0.16 ( 8) link_NAG-ASN : angle 2.53829 / 1.54 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 PHE cc_start: 0.5252 (m-80) cc_final: 0.5043 (m-80) REVERT: C 206 LYS cc_start: -0.1551 (mmtt) cc_final: -0.2681 (tttt) outliers start: 33 outliers final: 12 residues processed: 162 average time/residue: 0.6477 time to fit residues: 110.7174 Evaluate side-chains 83 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 194 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 121 ASN A 185 ASN A 271 GLN A 280 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN C 110 GLN D 38 GLN D 138 ASN E 77 ASN E 188 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.096341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.056265 restraints weight = 27916.602| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 5.08 r_work: 0.2814 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9146 Z= 0.128 Angle : 0.644 9.055 12475 Z= 0.329 Chirality : 0.045 0.208 1413 Planarity : 0.005 0.053 1589 Dihedral : 5.608 58.995 1417 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.21 % Favored : 95.70 % Rotamer: Outliers : 5.55 % Allowed : 28.76 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.51 (0.25), residues: 1139 helix: 1.41 (0.77), residues: 55 sheet: 1.46 (0.23), residues: 494 loop : -0.80 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 95 TYR 0.016 0.001 TYR C 193 PHE 0.013 0.001 PHE A 133 TRP 0.009 0.001 TRP A 258 HIS 0.005 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 9129) covalent geometry : angle 0.63644 / 0.33 (12433) SS BOND : bond 0.00545 / 0.25 ( 9) SS BOND : angle 1.56893 / 0.90 ( 18) hydrogen bonds : bond 0.03280 / 2.17 ( 322) hydrogen bonds : angle 4.96679 / 3.47 ( 882) link_NAG-ASN : bond 0.00266 / 0.16 ( 8) link_NAG-ASN : angle 2.00942 / 1.21 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 73 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.9430 (OUTLIER) cc_final: 0.9029 (p) REVERT: A 231 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8572 (pp) REVERT: A 276 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7620 (mp) REVERT: B 55 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8055 (t70) REVERT: B 59 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7892 (mp) REVERT: B 151 ASP cc_start: 0.8522 (m-30) cc_final: 0.8207 (p0) REVERT: C 52 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8366 (tp30) REVERT: D 123 GLU cc_start: 0.8713 (mp0) cc_final: 0.8469 (mp0) REVERT: D 195 GLU cc_start: 0.8929 (tt0) cc_final: 0.8404 (tp30) REVERT: E 57 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8540 (mt-10) REVERT: E 76 LYS cc_start: 0.9185 (mtmm) cc_final: 0.8931 (mtmm) REVERT: E 103 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7849 (tm-30) REVERT: E 165 GLU cc_start: 0.9294 (mt-10) cc_final: 0.9069 (mp0) REVERT: E 221 ASN cc_start: 0.9458 (t0) cc_final: 0.9217 (t0) outliers start: 55 outliers final: 21 residues processed: 124 average time/residue: 0.5578 time to fit residues: 73.6740 Evaluate side-chains 99 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 201 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 80 optimal weight: 0.0980 chunk 14 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 HIS A 148 ASN A 185 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 110 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.094120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.054521 restraints weight = 27757.466| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 4.71 r_work: 0.2763 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9146 Z= 0.197 Angle : 0.671 8.703 12475 Z= 0.343 Chirality : 0.046 0.228 1413 Planarity : 0.005 0.060 1589 Dihedral : 5.416 58.984 1405 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.92 % Favored : 95.00 % Rotamer: Outliers : 4.44 % Allowed : 29.06 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.40 (0.25), residues: 1139 helix: 1.03 (0.75), residues: 54 sheet: 1.31 (0.23), residues: 496 loop : -0.77 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 95 TYR 0.014 0.001 TYR B 27 PHE 0.020 0.001 PHE B 153 TRP 0.014 0.001 TRP A 258 HIS 0.005 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 ( 9129) covalent geometry : angle 0.65751 / 0.34 (12433) SS BOND : bond 0.00672 / 0.32 ( 9) SS BOND : angle 1.91244 / 1.13 ( 18) hydrogen bonds : bond 0.03901 / 2.57 ( 322) hydrogen bonds : angle 4.97393 / 3.47 ( 882) link_NAG-ASN : bond 0.00238 / 0.14 ( 8) link_NAG-ASN : angle 2.72567 / 1.60 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 73 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.9096 (p) REVERT: A 185 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.7960 (p0) REVERT: A 231 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8681 (pp) REVERT: B 59 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7686 (mp) REVERT: B 151 ASP cc_start: 0.8547 (m-30) cc_final: 0.8196 (p0) REVERT: D 4 MET cc_start: 0.9479 (mmm) cc_final: 0.9240 (mmm) REVERT: D 123 GLU cc_start: 0.8684 (mp0) cc_final: 0.8440 (mp0) REVERT: D 195 GLU cc_start: 0.8978 (tt0) cc_final: 0.8442 (tp30) REVERT: E 43 LYS cc_start: 0.9416 (mmmm) cc_final: 0.9097 (mmmm) REVERT: E 57 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8575 (mt-10) REVERT: E 76 LYS cc_start: 0.9189 (mtmm) cc_final: 0.8941 (mtmm) REVERT: E 165 GLU cc_start: 0.9265 (mt-10) cc_final: 0.9007 (mp0) REVERT: E 221 ASN cc_start: 0.9472 (t0) cc_final: 0.9258 (t0) outliers start: 44 outliers final: 23 residues processed: 110 average time/residue: 0.5613 time to fit residues: 65.7384 Evaluate side-chains 92 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 223 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 110 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN B 204 ASN C 110 GLN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN E 60 HIS E 74 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.094873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.055328 restraints weight = 28136.694| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 4.67 r_work: 0.2785 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9146 Z= 0.128 Angle : 0.637 8.307 12475 Z= 0.322 Chirality : 0.045 0.193 1413 Planarity : 0.004 0.056 1589 Dihedral : 5.186 58.042 1405 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.39 % Favored : 95.52 % Rotamer: Outliers : 4.14 % Allowed : 29.57 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.38 (0.25), residues: 1139 helix: 0.67 (0.75), residues: 54 sheet: 1.41 (0.23), residues: 492 loop : -0.84 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 63 TYR 0.011 0.001 TYR B 60 PHE 0.009 0.001 PHE A 92 TRP 0.010 0.001 TRP A 258 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 9129) covalent geometry : angle 0.62710 / 0.32 (12433) SS BOND : bond 0.00563 / 0.27 ( 9) SS BOND : angle 1.65241 / 0.97 ( 18) hydrogen bonds : bond 0.03238 / 2.15 ( 322) hydrogen bonds : angle 4.88067 / 3.39 ( 882) link_NAG-ASN : bond 0.00273 / 0.17 ( 8) link_NAG-ASN : angle 2.20243 / 1.31 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 74 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.9031 (p) REVERT: A 185 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8137 (p0) REVERT: A 231 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8595 (pp) REVERT: B 47 TRP cc_start: 0.7360 (p-90) cc_final: 0.7142 (p-90) REVERT: B 59 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7676 (mp) REVERT: B 151 ASP cc_start: 0.8654 (m-30) cc_final: 0.8290 (p0) REVERT: C 95 ARG cc_start: 0.8636 (tmm160) cc_final: 0.8396 (tmm160) REVERT: D 4 MET cc_start: 0.9463 (mmm) cc_final: 0.9159 (mmm) REVERT: D 123 GLU cc_start: 0.8702 (mp0) cc_final: 0.8486 (mp0) REVERT: D 167 ASP cc_start: 0.8467 (t0) cc_final: 0.8163 (t0) REVERT: D 195 GLU cc_start: 0.8954 (tt0) cc_final: 0.8443 (tp30) REVERT: E 57 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8519 (mt-10) REVERT: E 76 LYS cc_start: 0.9156 (mtmm) cc_final: 0.8904 (mtmm) outliers start: 41 outliers final: 23 residues processed: 111 average time/residue: 0.6399 time to fit residues: 75.4001 Evaluate side-chains 91 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 201 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 110 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN C 110 GLN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.093728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.053948 restraints weight = 28235.648| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 4.82 r_work: 0.2751 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9146 Z= 0.188 Angle : 0.670 8.783 12475 Z= 0.342 Chirality : 0.046 0.217 1413 Planarity : 0.005 0.059 1589 Dihedral : 5.306 58.619 1405 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.53 % Favored : 94.38 % Rotamer: Outliers : 4.34 % Allowed : 28.96 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.25 (0.25), residues: 1139 helix: 0.53 (0.75), residues: 54 sheet: 1.22 (0.23), residues: 492 loop : -0.82 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 63 TYR 0.013 0.001 TYR B 27 PHE 0.019 0.001 PHE B 153 TRP 0.013 0.001 TRP A 258 HIS 0.005 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 ( 9129) covalent geometry : angle 0.66076 / 0.34 (12433) SS BOND : bond 0.00634 / 0.30 ( 9) SS BOND : angle 1.82429 / 1.09 ( 18) hydrogen bonds : bond 0.03762 / 2.47 ( 322) hydrogen bonds : angle 4.92514 / 3.43 ( 882) link_NAG-ASN : bond 0.00264 / 0.14 ( 8) link_NAG-ASN : angle 2.13617 / 1.31 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 64 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 114 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.9035 (p) REVERT: A 185 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8309 (p0) REVERT: A 231 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8700 (pp) REVERT: B 47 TRP cc_start: 0.7477 (p-90) cc_final: 0.7166 (p-90) REVERT: B 59 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7662 (mp) REVERT: B 151 ASP cc_start: 0.8706 (m-30) cc_final: 0.8371 (p0) REVERT: D 4 MET cc_start: 0.9483 (mmm) cc_final: 0.9241 (mmm) REVERT: D 167 ASP cc_start: 0.8560 (t0) cc_final: 0.8229 (t0) REVERT: D 170 ASP cc_start: 0.8650 (p0) cc_final: 0.8437 (p0) REVERT: D 181 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7806 (mp) REVERT: E 43 LYS cc_start: 0.9381 (mmmm) cc_final: 0.9125 (mmmm) REVERT: E 57 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8570 (mt-10) REVERT: E 76 LYS cc_start: 0.9170 (mtmm) cc_final: 0.8917 (mtmm) outliers start: 43 outliers final: 24 residues processed: 102 average time/residue: 0.5484 time to fit residues: 59.7089 Evaluate side-chains 90 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 201 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 44 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN C 16 GLN C 110 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.092518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.052754 restraints weight = 28056.052| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 4.65 r_work: 0.2723 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 9146 Z= 0.246 Angle : 0.719 9.815 12475 Z= 0.370 Chirality : 0.047 0.238 1413 Planarity : 0.005 0.064 1589 Dihedral : 5.515 54.974 1405 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.79 % Favored : 94.12 % Rotamer: Outliers : 5.15 % Allowed : 28.15 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.17 (0.25), residues: 1139 helix: 0.58 (0.75), residues: 55 sheet: 1.12 (0.23), residues: 493 loop : -0.84 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 95 TYR 0.015 0.001 TYR B 27 PHE 0.014 0.001 PHE A 92 TRP 0.015 0.001 TRP A 258 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.25 ( 9129) covalent geometry : angle 0.70980 / 0.37 (12433) SS BOND : bond 0.00715 / 0.34 ( 9) SS BOND : angle 1.93679 / 1.17 ( 18) hydrogen bonds : bond 0.04257 / 2.80 ( 322) hydrogen bonds : angle 5.09189 / 3.56 ( 882) link_NAG-ASN : bond 0.00292 / 0.14 ( 8) link_NAG-ASN : angle 2.16884 / 1.36 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 66 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.9022 (p) REVERT: A 185 ASN cc_start: 0.9024 (OUTLIER) cc_final: 0.8386 (p0) REVERT: A 231 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8758 (pp) REVERT: B 10 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7989 (pm20) REVERT: B 47 TRP cc_start: 0.7562 (p-90) cc_final: 0.7226 (p-90) REVERT: B 59 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7583 (mp) REVERT: C 196 GLN cc_start: 0.7122 (mm-40) cc_final: 0.6485 (mp-120) REVERT: D 167 ASP cc_start: 0.8525 (t0) cc_final: 0.8200 (t0) REVERT: D 170 ASP cc_start: 0.8686 (p0) cc_final: 0.8471 (p0) REVERT: D 195 GLU cc_start: 0.9043 (tt0) cc_final: 0.8396 (tp30) REVERT: E 43 LYS cc_start: 0.9427 (mmmm) cc_final: 0.9142 (mmmm) REVERT: E 57 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8634 (mt-10) REVERT: E 76 LYS cc_start: 0.9188 (mtmm) cc_final: 0.8974 (mtmm) REVERT: E 227 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8549 (ttm170) outliers start: 51 outliers final: 27 residues processed: 112 average time/residue: 0.5646 time to fit residues: 67.3801 Evaluate side-chains 94 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 61 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 223 LYS Chi-restraints excluded: chain E residue 227 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 71 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 GLN C 110 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.093682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054695 restraints weight = 28211.738| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 4.43 r_work: 0.2765 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9146 Z= 0.135 Angle : 0.682 10.478 12475 Z= 0.344 Chirality : 0.045 0.203 1413 Planarity : 0.004 0.059 1589 Dihedral : 5.253 55.816 1405 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 3.73 % Allowed : 29.87 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.24 (0.25), residues: 1139 helix: 0.61 (0.75), residues: 55 sheet: 1.22 (0.23), residues: 494 loop : -0.85 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 63 TYR 0.011 0.001 TYR C 142 PHE 0.010 0.001 PHE B 64 TRP 0.010 0.001 TRP A 258 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 9129) covalent geometry : angle 0.67616 / 0.34 (12433) SS BOND : bond 0.00557 / 0.28 ( 9) SS BOND : angle 1.42689 / 0.89 ( 18) hydrogen bonds : bond 0.03368 / 2.26 ( 322) hydrogen bonds : angle 4.93630 / 3.44 ( 882) link_NAG-ASN : bond 0.00272 / 0.17 ( 8) link_NAG-ASN : angle 1.86184 / 1.17 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 114 THR cc_start: 0.9338 (OUTLIER) cc_final: 0.9030 (p) REVERT: A 185 ASN cc_start: 0.8785 (p0) cc_final: 0.8431 (p0) REVERT: A 231 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8669 (pp) REVERT: B 10 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7977 (pm20) REVERT: B 47 TRP cc_start: 0.7416 (p-90) cc_final: 0.7177 (p-90) REVERT: B 59 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7696 (mp) REVERT: C 196 GLN cc_start: 0.6592 (mm-40) cc_final: 0.6134 (mm-40) REVERT: D 167 ASP cc_start: 0.8549 (t0) cc_final: 0.8218 (t0) REVERT: D 195 GLU cc_start: 0.8991 (tt0) cc_final: 0.8412 (tp30) REVERT: E 43 LYS cc_start: 0.9402 (mmmm) cc_final: 0.9118 (mmmm) REVERT: E 57 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8525 (mt-10) REVERT: E 76 LYS cc_start: 0.9159 (mtmm) cc_final: 0.8936 (mtmm) REVERT: E 227 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8626 (ttt90) outliers start: 37 outliers final: 21 residues processed: 99 average time/residue: 0.6296 time to fit residues: 66.3149 Evaluate side-chains 87 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 227 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 47 optimal weight: 30.0000 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 20.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 GLN C 110 GLN D 152 ASN E 221 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.092270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.053506 restraints weight = 28069.587| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 4.40 r_work: 0.2723 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 9146 Z= 0.230 Angle : 0.752 11.081 12475 Z= 0.386 Chirality : 0.047 0.247 1413 Planarity : 0.005 0.062 1589 Dihedral : 5.470 52.141 1404 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.06 % Favored : 93.85 % Rotamer: Outliers : 3.63 % Allowed : 30.17 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.16 (0.25), residues: 1139 helix: 0.64 (0.76), residues: 55 sheet: 1.07 (0.23), residues: 514 loop : -0.89 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 16 TYR 0.014 0.001 TYR B 27 PHE 0.019 0.001 PHE B 153 TRP 0.014 0.001 TRP A 258 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.23 ( 9129) covalent geometry : angle 0.74490 / 0.38 (12433) SS BOND : bond 0.00691 / 0.32 ( 9) SS BOND : angle 1.87170 / 1.15 ( 18) hydrogen bonds : bond 0.04244 / 2.83 ( 322) hydrogen bonds : angle 5.10302 / 3.56 ( 882) link_NAG-ASN : bond 0.00286 / 0.15 ( 8) link_NAG-ASN : angle 2.04039 / 1.32 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 65 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.8992 (p) REVERT: A 185 ASN cc_start: 0.8844 (p0) cc_final: 0.8319 (p0) REVERT: B 10 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7969 (pm20) REVERT: B 63 ARG cc_start: 0.8568 (tmm160) cc_final: 0.8329 (tpt90) REVERT: D 167 ASP cc_start: 0.8654 (t0) cc_final: 0.8245 (t0) REVERT: D 195 GLU cc_start: 0.9045 (tt0) cc_final: 0.8378 (tp30) REVERT: E 43 LYS cc_start: 0.9438 (mmmm) cc_final: 0.9169 (mmmm) REVERT: E 57 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8601 (mt-10) REVERT: E 76 LYS cc_start: 0.9185 (mtmm) cc_final: 0.8952 (mtmm) outliers start: 36 outliers final: 23 residues processed: 98 average time/residue: 0.6371 time to fit residues: 66.3286 Evaluate side-chains 86 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 201 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 52 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 20 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 23 optimal weight: 0.0970 chunk 45 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 108 optimal weight: 0.0470 chunk 32 optimal weight: 0.0040 chunk 75 optimal weight: 0.7980 overall best weight: 0.2888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 GLN B 65 GLN C 110 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.094845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.055805 restraints weight = 27917.498| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 4.52 r_work: 0.2793 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9146 Z= 0.123 Angle : 0.703 11.641 12475 Z= 0.351 Chirality : 0.045 0.260 1413 Planarity : 0.004 0.053 1589 Dihedral : 5.021 51.952 1404 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 2.02 % Allowed : 31.79 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.34 (0.25), residues: 1139 helix: 0.67 (0.77), residues: 55 sheet: 1.52 (0.23), residues: 487 loop : -1.00 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 95 TYR 0.013 0.001 TYR B 60 PHE 0.013 0.001 PHE B 64 TRP 0.007 0.001 TRP E 47 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 ( 9129) covalent geometry : angle 0.69587 / 0.35 (12433) SS BOND : bond 0.00398 / 0.18 ( 9) SS BOND : angle 1.12573 / 0.74 ( 18) hydrogen bonds : bond 0.02824 / 1.92 ( 322) hydrogen bonds : angle 4.83341 / 3.36 ( 882) link_NAG-ASN : bond 0.00343 / 0.21 ( 8) link_NAG-ASN : angle 2.17346 / 1.40 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 14 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8421 (mm-40) REVERT: A 114 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.8856 (p) REVERT: A 231 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8554 (pp) REVERT: B 10 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7934 (pm20) REVERT: B 65 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.8597 (mm110) REVERT: C 185 GLU cc_start: 0.8724 (mp0) cc_final: 0.8325 (pp20) REVERT: D 167 ASP cc_start: 0.8710 (t0) cc_final: 0.8263 (t0) REVERT: D 170 ASP cc_start: 0.8916 (p0) cc_final: 0.8700 (p0) REVERT: D 195 GLU cc_start: 0.8951 (tt0) cc_final: 0.8340 (tp30) REVERT: E 57 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8466 (mt-10) REVERT: E 76 LYS cc_start: 0.9104 (mtmm) cc_final: 0.8868 (mtmm) outliers start: 20 outliers final: 10 residues processed: 83 average time/residue: 0.7040 time to fit residues: 61.4851 Evaluate side-chains 73 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 40.0000 chunk 33 optimal weight: 0.3980 chunk 89 optimal weight: 6.9990 chunk 19 optimal weight: 0.0170 chunk 54 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 30.0000 chunk 23 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 93 optimal weight: 0.1980 overall best weight: 0.4620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 GLN D 152 ASN E 221 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.094524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.055079 restraints weight = 27423.654| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 4.66 r_work: 0.2796 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9146 Z= 0.129 Angle : 0.721 11.099 12475 Z= 0.364 Chirality : 0.045 0.260 1413 Planarity : 0.004 0.052 1589 Dihedral : 5.009 54.166 1404 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.39 % Favored : 95.52 % Rotamer: Outliers : 1.72 % Allowed : 32.39 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.38 (0.25), residues: 1139 helix: 0.61 (0.76), residues: 55 sheet: 1.68 (0.23), residues: 479 loop : -1.05 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 95 TYR 0.010 0.001 TYR B 60 PHE 0.016 0.001 PHE B 153 TRP 0.070 0.001 TRP B 47 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 9129) covalent geometry : angle 0.71571 / 0.36 (12433) SS BOND : bond 0.00422 / 0.20 ( 9) SS BOND : angle 1.25261 / 0.79 ( 18) hydrogen bonds : bond 0.02868 / 1.95 ( 322) hydrogen bonds : angle 4.79961 / 3.34 ( 882) link_NAG-ASN : bond 0.00279 / 0.19 ( 8) link_NAG-ASN : angle 2.00485 / 1.30 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.8834 (p) REVERT: A 169 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8841 (tm-30) REVERT: A 231 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8549 (pp) REVERT: B 10 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: B 65 GLN cc_start: 0.9245 (pm20) cc_final: 0.8710 (mm110) REVERT: C 185 GLU cc_start: 0.8762 (mp0) cc_final: 0.8468 (pp20) REVERT: C 186 GLN cc_start: 0.2490 (OUTLIER) cc_final: 0.1885 (pm20) REVERT: D 167 ASP cc_start: 0.8712 (t0) cc_final: 0.8270 (t0) REVERT: D 170 ASP cc_start: 0.8899 (p0) cc_final: 0.8695 (p0) REVERT: D 195 GLU cc_start: 0.8937 (tt0) cc_final: 0.8348 (tp30) REVERT: E 57 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8431 (mt-10) REVERT: E 76 LYS cc_start: 0.9121 (mtmm) cc_final: 0.8886 (mtmm) outliers start: 17 outliers final: 11 residues processed: 74 average time/residue: 0.7387 time to fit residues: 57.7087 Evaluate side-chains 74 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 78 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 0.0170 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.094355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.055147 restraints weight = 27541.805| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 4.43 r_work: 0.2785 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9146 Z= 0.129 Angle : 0.704 11.541 12475 Z= 0.353 Chirality : 0.045 0.230 1413 Planarity : 0.004 0.051 1589 Dihedral : 4.898 54.623 1404 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.09 % Favored : 94.82 % Rotamer: Outliers : 1.82 % Allowed : 32.59 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.43 (0.25), residues: 1139 helix: 0.65 (0.76), residues: 55 sheet: 1.66 (0.23), residues: 483 loop : -0.98 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 95 TYR 0.010 0.001 TYR B 60 PHE 0.009 0.001 PHE B 129 TRP 0.038 0.001 TRP B 47 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 9129) covalent geometry : angle 0.69899 / 0.35 (12433) SS BOND : bond 0.00467 / 0.21 ( 9) SS BOND : angle 1.28944 / 0.83 ( 18) hydrogen bonds : bond 0.02952 / 1.97 ( 322) hydrogen bonds : angle 4.72631 / 3.30 ( 882) link_NAG-ASN : bond 0.00277 / 0.18 ( 8) link_NAG-ASN : angle 1.86276 / 1.20 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4193.51 seconds wall clock time: 72 minutes 20.13 seconds (4340.13 seconds total)