Starting phenix.real_space_refine on Sat Aug 23 01:35:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kfz_37209/08_2025/8kfz_37209.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kfz_37209/08_2025/8kfz_37209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kfz_37209/08_2025/8kfz_37209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kfz_37209/08_2025/8kfz_37209.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kfz_37209/08_2025/8kfz_37209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kfz_37209/08_2025/8kfz_37209.map" } resolution = 3.3 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= 0.001 sd= 0.023 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 66 5.16 5 C 5733 2.51 5 N 1503 2.21 5 O 1664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8966 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2342 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 5, 'TRANS': 282} Chain: "A" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1812 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Time building chain proxies: 2.32, per 1000 atoms: 0.26 Number of scatterers: 8966 At special positions: 0 Unit cell: (87.36, 122.72, 125.84, 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 66 16.00 O 1664 8.00 N 1503 7.00 C 5733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 345.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 39.2% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'R' and resid 30 through 62 Processing helix chain 'R' and resid 68 through 86 Processing helix chain 'R' and resid 86 through 97 removed outlier: 4.228A pdb=" N PHE R 90 " --> pdb=" O PHE R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 137 through 145 removed outlier: 5.113A pdb=" N LYS R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 170 Proline residue: R 167 - end of helix Processing helix chain 'R' and resid 188 through 205 removed outlier: 4.142A pdb=" N LYS R 193 " --> pdb=" O GLN R 189 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TRP R 194 " --> pdb=" O GLN R 190 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN R 203 " --> pdb=" O ASN R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 227 removed outlier: 3.704A pdb=" N ILE R 213 " --> pdb=" O ILE R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 250 removed outlier: 3.550A pdb=" N LEU R 248 " --> pdb=" O VAL R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 266 removed outlier: 3.914A pdb=" N ASN R 255 " --> pdb=" O TRP R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 290 Processing helix chain 'R' and resid 291 through 301 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.017A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.944A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.566A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.596A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.819A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.542A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.855A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.566A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 172 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.523A pdb=" N HIS A 322 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.882A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.590A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.277A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.984A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.086A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.702A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 5.704A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.258A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.258A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.465A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 135 through 136 removed outlier: 3.591A pdb=" N GLN S 219 " --> pdb=" O THR S 226 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1398 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: 1.56 Time building geometry restraints manager: 1.17 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: 2859 1.34 - 1.46: 2059 1.46 - 1.58: 4140 1.58 - 1.70: 1 1.70 - 1.81: 95 Bond restraints: 9154 Sorted by residual: bond pdb=" N PRO S 169 " pdb=" CD PRO S 169 " ideal model delta sigma weight residual 1.473 1.418 0.055 1.40e-02 5.10e+03 1.54e+01 bond pdb=" CB PRO S 169 " pdb=" CG PRO S 169 " ideal model delta sigma weight residual 1.492 1.593 -0.101 5.00e-02 4.00e+02 4.11e+00 bond pdb=" CG PRO S 169 " pdb=" CD PRO S 169 " ideal model delta sigma weight residual 1.503 1.552 -0.049 3.40e-02 8.65e+02 2.12e+00 bond pdb=" CB MET S 218 " pdb=" CG MET S 218 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.27e+00 bond pdb=" C VAL A 201 " pdb=" O VAL A 201 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.19e+00 ... (remaining 9149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 12233 2.46 - 4.92: 135 4.92 - 7.38: 16 7.38 - 9.85: 4 9.85 - 12.31: 2 Bond angle restraints: 12390 Sorted by residual: angle pdb=" CA PRO S 169 " pdb=" N PRO S 169 " pdb=" CD PRO S 169 " ideal model delta sigma weight residual 112.00 118.38 -6.38 1.40e+00 5.10e-01 2.08e+01 angle pdb=" C VAL R 85 " pdb=" N PHE R 86 " pdb=" CA PHE R 86 " ideal model delta sigma weight residual 120.28 114.93 5.35 1.44e+00 4.82e-01 1.38e+01 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 128.62 -7.08 1.91e+00 2.74e-01 1.37e+01 angle pdb=" CA LEU R 159 " pdb=" CB LEU R 159 " pdb=" CG LEU R 159 " ideal model delta sigma weight residual 116.30 128.61 -12.31 3.50e+00 8.16e-02 1.24e+01 angle pdb=" N PHE R 86 " pdb=" CA PHE R 86 " pdb=" CB PHE R 86 " ideal model delta sigma weight residual 110.22 115.51 -5.29 1.54e+00 4.22e-01 1.18e+01 ... (remaining 12385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4739 17.90 - 35.81: 526 35.81 - 53.71: 140 53.71 - 71.61: 16 71.61 - 89.52: 2 Dihedral angle restraints: 5423 sinusoidal: 2109 harmonic: 3314 Sorted by residual: dihedral pdb=" CA PHE R 290 " pdb=" C PHE R 290 " pdb=" N THR R 291 " pdb=" CA THR R 291 " ideal model delta harmonic sigma weight residual 180.00 151.21 28.79 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA MET R 266 " pdb=" C MET R 266 " pdb=" N HIS R 267 " pdb=" CA HIS R 267 " ideal model delta harmonic sigma weight residual 180.00 155.48 24.52 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ASN S 159 " pdb=" C ASN S 159 " pdb=" N THR S 160 " pdb=" CA THR S 160 " ideal model delta harmonic sigma weight residual 180.00 161.86 18.14 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1270 0.072 - 0.145: 135 0.145 - 0.217: 8 0.217 - 0.290: 0 0.290 - 0.362: 1 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CB ILE R 115 " pdb=" CA ILE R 115 " pdb=" CG1 ILE R 115 " pdb=" CG2 ILE R 115 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CG LEU A 268 " pdb=" CB LEU A 268 " pdb=" CD1 LEU A 268 " pdb=" CD2 LEU A 268 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL A 339 " pdb=" CA VAL A 339 " pdb=" CG1 VAL A 339 " pdb=" CG2 VAL A 339 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 1411 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 251 " -0.026 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP R 251 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP R 251 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP R 251 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 251 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 251 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP R 251 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 251 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 251 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP R 251 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 86 " 0.029 2.00e-02 2.50e+03 2.46e-02 1.05e+01 pdb=" CG PHE R 86 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE R 86 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE R 86 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE R 86 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE R 86 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE R 86 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.57e+00 pdb=" N PRO C 49 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.029 5.00e-02 4.00e+02 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1029 2.75 - 3.28: 9143 3.28 - 3.82: 15574 3.82 - 4.36: 18629 4.36 - 4.90: 31446 Nonbonded interactions: 75821 Sorted by model distance: nonbonded pdb=" O SER S 85 " pdb=" NH1 ARG S 87 " model vdw 2.206 3.120 nonbonded pdb=" ND1 HIS B 311 " pdb=" OG SER B 331 " model vdw 2.233 3.120 nonbonded pdb=" O LYS R 306 " pdb=" ND1 HIS R 310 " model vdw 2.257 3.120 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.258 3.040 nonbonded pdb=" O PHE R 88 " pdb=" OG1 THR R 92 " model vdw 2.259 3.040 ... (remaining 75816 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.170 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 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 : 0.004 0.101 9157 Z= 0.171 Angle : 0.667 12.307 12396 Z= 0.356 Chirality : 0.045 0.362 1414 Planarity : 0.004 0.053 1554 Dihedral : 15.611 89.516 3276 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.10 % Allowed : 28.85 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.79 (0.25), residues: 1125 helix: 1.73 (0.26), residues: 399 sheet: 0.05 (0.29), residues: 284 loop : -0.16 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 219 TYR 0.022 0.002 TYR S 178 PHE 0.056 0.002 PHE R 86 TRP 0.060 0.002 TRP R 251 HIS 0.004 0.001 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9154) covalent geometry : angle 0.66738 (12390) SS BOND : bond 0.00187 ( 3) SS BOND : angle 0.37868 ( 6) hydrogen bonds : bond 0.13646 ( 487) hydrogen bonds : angle 6.45577 ( 1398) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 0.331 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: symmetry clash REVERT: R 121 MET cc_start: 0.7320 (mmt) cc_final: 0.7027 (mmt) REVERT: R 131 ARG cc_start: 0.8128 (mtt180) cc_final: 0.7923 (mtt180) REVERT: R 132 TYR cc_start: 0.8680 (t80) cc_final: 0.8449 (t80) REVERT: B 57 LYS cc_start: 0.7624 (mtmt) cc_final: 0.7149 (mtmt) REVERT: B 130 GLU cc_start: 0.7745 (mp0) cc_final: 0.7298 (mp0) REVERT: B 169 TRP cc_start: 0.7798 (m100) cc_final: 0.7593 (m100) REVERT: S 38 ARG cc_start: 0.7426 (ptt180) cc_final: 0.7033 (ptt180) REVERT: S 90 ASP cc_start: 0.7234 (m-30) cc_final: 0.6981 (m-30) REVERT: S 167 GLN cc_start: 0.8221 (tt0) cc_final: 0.7952 (tp40) outliers start: 1 outliers final: 1 residues processed: 304 average time/residue: 0.1268 time to fit residues: 50.1736 Evaluate side-chains 292 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 183 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.0370 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 31 GLN R 76 ASN R 230 ASN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 155 ASN B 239 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.156782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128483 restraints weight = 15253.756| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.70 r_work: 0.3514 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9157 Z= 0.157 Angle : 0.612 8.570 12396 Z= 0.326 Chirality : 0.043 0.236 1414 Planarity : 0.004 0.051 1554 Dihedral : 4.729 27.704 1227 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.54 % Allowed : 25.10 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.88 (0.25), residues: 1125 helix: 1.84 (0.26), residues: 401 sheet: 0.23 (0.29), residues: 287 loop : -0.28 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 18 TYR 0.017 0.002 TYR R 118 PHE 0.042 0.002 PHE R 86 TRP 0.034 0.002 TRP R 251 HIS 0.005 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9154) covalent geometry : angle 0.61232 (12390) SS BOND : bond 0.00239 ( 3) SS BOND : angle 0.55086 ( 6) hydrogen bonds : bond 0.04882 ( 487) hydrogen bonds : angle 5.47820 ( 1398) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 296 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 PHE cc_start: 0.7178 (m-80) cc_final: 0.6711 (m-80) REVERT: R 121 MET cc_start: 0.7409 (mmt) cc_final: 0.6654 (mmt) REVERT: R 220 LYS cc_start: 0.8277 (mmmm) cc_final: 0.7911 (mmmm) REVERT: A 197 LYS cc_start: 0.7400 (mtmt) cc_final: 0.7015 (mtmt) REVERT: A 243 MET cc_start: 0.8399 (mmm) cc_final: 0.7751 (tpp) REVERT: A 336 PHE cc_start: 0.7959 (t80) cc_final: 0.7654 (t80) REVERT: A 349 LYS cc_start: 0.7936 (mtmt) cc_final: 0.7586 (ttmt) REVERT: B 130 GLU cc_start: 0.7926 (mp0) cc_final: 0.7553 (mp0) REVERT: B 183 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.7019 (t-170) REVERT: B 296 VAL cc_start: 0.7989 (t) cc_final: 0.7768 (m) REVERT: S 18 ARG cc_start: 0.7104 (tmm-80) cc_final: 0.6901 (ttp80) REVERT: S 38 ARG cc_start: 0.7446 (ptt180) cc_final: 0.7042 (ptt180) REVERT: S 90 ASP cc_start: 0.7283 (m-30) cc_final: 0.6982 (m-30) REVERT: S 171 GLN cc_start: 0.6514 (mm-40) cc_final: 0.6273 (tm-30) outliers start: 35 outliers final: 24 residues processed: 308 average time/residue: 0.1065 time to fit residues: 43.7405 Evaluate side-chains 320 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 295 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 0.2980 chunk 24 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 220 GLN B 295 ASN ** S 155 HIS ** 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 = 0.4054 r_free = 0.4054 target = 0.155640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.126521 restraints weight = 15161.131| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.73 r_work: 0.3506 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9157 Z= 0.214 Angle : 0.617 11.189 12396 Z= 0.331 Chirality : 0.043 0.178 1414 Planarity : 0.004 0.052 1554 Dihedral : 4.860 28.205 1227 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.25 % Allowed : 24.90 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.73 (0.25), residues: 1125 helix: 1.75 (0.26), residues: 407 sheet: 0.02 (0.29), residues: 286 loop : -0.31 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 219 TYR 0.014 0.002 TYR R 300 PHE 0.031 0.002 PHE R 86 TRP 0.027 0.002 TRP R 251 HIS 0.004 0.001 HIS R 310 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 9154) covalent geometry : angle 0.61707 (12390) SS BOND : bond 0.00228 ( 3) SS BOND : angle 0.56493 ( 6) hydrogen bonds : bond 0.04862 ( 487) hydrogen bonds : angle 5.44688 ( 1398) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 303 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 PHE cc_start: 0.7449 (m-80) cc_final: 0.6860 (m-80) REVERT: R 121 MET cc_start: 0.7423 (mmt) cc_final: 0.6724 (mmt) REVERT: A 197 LYS cc_start: 0.7374 (mtmt) cc_final: 0.7050 (mtmt) REVERT: A 321 THR cc_start: 0.8332 (m) cc_final: 0.7969 (t) REVERT: A 336 PHE cc_start: 0.7941 (t80) cc_final: 0.7606 (t80) REVERT: A 349 LYS cc_start: 0.7958 (mtmt) cc_final: 0.7589 (ttmt) REVERT: B 130 GLU cc_start: 0.7987 (mp0) cc_final: 0.7661 (mp0) REVERT: B 183 HIS cc_start: 0.8031 (OUTLIER) cc_final: 0.7114 (t-170) REVERT: B 292 PHE cc_start: 0.7855 (m-10) cc_final: 0.7528 (m-10) REVERT: B 313 ASN cc_start: 0.7866 (t0) cc_final: 0.7500 (t0) REVERT: S 38 ARG cc_start: 0.7530 (ptt180) cc_final: 0.7177 (ptt180) REVERT: S 90 ASP cc_start: 0.7339 (m-30) cc_final: 0.7030 (m-30) outliers start: 42 outliers final: 31 residues processed: 318 average time/residue: 0.1025 time to fit residues: 43.5327 Evaluate side-chains 330 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 298 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 204 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 68 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 HIS ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 13 GLN B 155 ASN B 220 GLN B 237 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.156331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.127259 restraints weight = 15305.017| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.75 r_work: 0.3495 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9157 Z= 0.161 Angle : 0.592 11.724 12396 Z= 0.314 Chirality : 0.043 0.268 1414 Planarity : 0.004 0.051 1554 Dihedral : 4.714 28.513 1227 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.25 % Allowed : 25.20 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.78 (0.25), residues: 1125 helix: 1.90 (0.26), residues: 401 sheet: 0.01 (0.29), residues: 286 loop : -0.35 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.011 0.001 TYR B 289 PHE 0.021 0.002 PHE R 86 TRP 0.028 0.002 TRP R 251 HIS 0.005 0.001 HIS R 310 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9154) covalent geometry : angle 0.59160 (12390) SS BOND : bond 0.00206 ( 3) SS BOND : angle 0.48371 ( 6) hydrogen bonds : bond 0.04456 ( 487) hydrogen bonds : angle 5.26594 ( 1398) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 295 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 73 TYR cc_start: 0.7330 (m-10) cc_final: 0.7075 (m-10) REVERT: R 86 PHE cc_start: 0.7493 (m-80) cc_final: 0.6975 (m-80) REVERT: R 121 MET cc_start: 0.7405 (mmt) cc_final: 0.6815 (mmt) REVERT: R 149 MET cc_start: 0.7330 (tpt) cc_final: 0.6803 (tpt) REVERT: R 159 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6893 (mp) REVERT: R 220 LYS cc_start: 0.8230 (mmmm) cc_final: 0.7911 (mmmm) REVERT: A 197 LYS cc_start: 0.7345 (mtmt) cc_final: 0.6996 (mtmt) REVERT: A 321 THR cc_start: 0.8309 (m) cc_final: 0.7968 (t) REVERT: A 349 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7671 (ttmt) REVERT: B 13 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.7008 (pp30) REVERT: B 14 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7439 (mt) REVERT: B 130 GLU cc_start: 0.7988 (mp0) cc_final: 0.7582 (mp0) REVERT: B 134 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7314 (mtm-85) REVERT: B 183 HIS cc_start: 0.8041 (OUTLIER) cc_final: 0.7190 (t-170) REVERT: S 18 ARG cc_start: 0.7271 (tmm-80) cc_final: 0.7044 (tmm-80) REVERT: S 38 ARG cc_start: 0.7490 (ptt180) cc_final: 0.7101 (ptt180) REVERT: S 90 ASP cc_start: 0.7342 (m-30) cc_final: 0.7041 (m-30) outliers start: 42 outliers final: 29 residues processed: 316 average time/residue: 0.1063 time to fit residues: 45.1566 Evaluate side-chains 324 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 290 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 230 ASN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 155 ASN B 295 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.156800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.127904 restraints weight = 15360.939| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.73 r_work: 0.3517 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9157 Z= 0.156 Angle : 0.599 12.453 12396 Z= 0.314 Chirality : 0.043 0.286 1414 Planarity : 0.004 0.052 1554 Dihedral : 4.676 28.802 1227 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.76 % Allowed : 26.21 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.73 (0.25), residues: 1125 helix: 1.78 (0.26), residues: 407 sheet: -0.03 (0.29), residues: 286 loop : -0.31 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.012 0.001 TYR S 178 PHE 0.035 0.002 PHE R 88 TRP 0.026 0.001 TRP R 251 HIS 0.004 0.001 HIS R 310 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9154) covalent geometry : angle 0.59881 (12390) SS BOND : bond 0.00220 ( 3) SS BOND : angle 0.51886 ( 6) hydrogen bonds : bond 0.04439 ( 487) hydrogen bonds : angle 5.21580 ( 1398) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 286 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 PHE cc_start: 0.7446 (m-80) cc_final: 0.6846 (m-80) REVERT: R 118 TYR cc_start: 0.6911 (m-80) cc_final: 0.6334 (m-80) REVERT: R 121 MET cc_start: 0.7462 (mmt) cc_final: 0.6722 (mmt) REVERT: R 149 MET cc_start: 0.7355 (tpt) cc_final: 0.7113 (tpt) REVERT: R 159 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6901 (mp) REVERT: R 207 LEU cc_start: 0.5297 (OUTLIER) cc_final: 0.4901 (tt) REVERT: R 211 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.6494 (m-80) REVERT: R 220 LYS cc_start: 0.8210 (mmmm) cc_final: 0.7831 (mmmm) REVERT: R 249 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6499 (mm) REVERT: A 197 LYS cc_start: 0.7403 (mtmt) cc_final: 0.7009 (mtmt) REVERT: A 321 THR cc_start: 0.8322 (m) cc_final: 0.8008 (t) REVERT: A 349 LYS cc_start: 0.7851 (mtmt) cc_final: 0.7576 (ttmt) REVERT: B 52 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7267 (mmm-85) REVERT: B 130 GLU cc_start: 0.7960 (mp0) cc_final: 0.7582 (mp0) REVERT: B 134 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7338 (mtm-85) REVERT: B 163 ASP cc_start: 0.6826 (p0) cc_final: 0.6581 (p0) REVERT: B 175 GLN cc_start: 0.7140 (mm-40) cc_final: 0.6894 (mm-40) REVERT: B 183 HIS cc_start: 0.8069 (OUTLIER) cc_final: 0.7216 (t-170) REVERT: S 18 ARG cc_start: 0.7231 (tmm-80) cc_final: 0.7003 (tmm-80) REVERT: S 38 ARG cc_start: 0.7481 (ptt180) cc_final: 0.7131 (ptt180) REVERT: S 90 ASP cc_start: 0.7331 (m-30) cc_final: 0.7025 (m-30) outliers start: 47 outliers final: 32 residues processed: 313 average time/residue: 0.1053 time to fit residues: 44.3689 Evaluate side-chains 333 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 294 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 211 PHE Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 101 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 155 ASN B 239 ASN ** S 155 HIS ** 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 = 0.4053 r_free = 0.4053 target = 0.155905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.127157 restraints weight = 15308.872| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.70 r_work: 0.3505 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9157 Z= 0.199 Angle : 0.621 13.220 12396 Z= 0.326 Chirality : 0.044 0.237 1414 Planarity : 0.004 0.052 1554 Dihedral : 4.765 28.883 1227 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.47 % Allowed : 25.61 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.62 (0.25), residues: 1125 helix: 1.74 (0.26), residues: 407 sheet: -0.12 (0.29), residues: 284 loop : -0.41 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 98 TYR 0.017 0.002 TYR R 300 PHE 0.028 0.002 PHE R 88 TRP 0.029 0.002 TRP R 251 HIS 0.004 0.001 HIS R 310 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 9154) covalent geometry : angle 0.62124 (12390) SS BOND : bond 0.00229 ( 3) SS BOND : angle 0.51717 ( 6) hydrogen bonds : bond 0.04580 ( 487) hydrogen bonds : angle 5.26872 ( 1398) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 298 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 PHE cc_start: 0.7524 (m-80) cc_final: 0.6908 (m-80) REVERT: R 118 TYR cc_start: 0.6931 (m-80) cc_final: 0.6431 (m-80) REVERT: R 121 MET cc_start: 0.7453 (mmt) cc_final: 0.6711 (mmt) REVERT: R 149 MET cc_start: 0.7363 (tpt) cc_final: 0.7088 (tpt) REVERT: R 159 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6891 (mp) REVERT: R 207 LEU cc_start: 0.5328 (OUTLIER) cc_final: 0.4914 (tt) REVERT: R 211 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6503 (m-80) REVERT: R 249 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6534 (mm) REVERT: R 306 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7051 (pttm) REVERT: A 197 LYS cc_start: 0.7403 (mtmt) cc_final: 0.6992 (mtmt) REVERT: A 321 THR cc_start: 0.8363 (m) cc_final: 0.8036 (t) REVERT: A 349 LYS cc_start: 0.7843 (mtmt) cc_final: 0.7509 (ttmt) REVERT: B 52 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7285 (mmm-85) REVERT: B 130 GLU cc_start: 0.7957 (mp0) cc_final: 0.7583 (mp0) REVERT: B 134 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7342 (mtm-85) REVERT: B 163 ASP cc_start: 0.6842 (p0) cc_final: 0.6629 (p0) REVERT: B 175 GLN cc_start: 0.7177 (mm-40) cc_final: 0.6860 (mm-40) REVERT: B 183 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.7274 (t-170) REVERT: S 38 ARG cc_start: 0.7550 (ptt180) cc_final: 0.7285 (ptt180) REVERT: S 90 ASP cc_start: 0.7345 (m-30) cc_final: 0.7085 (m-30) REVERT: S 215 TYR cc_start: 0.7981 (m-10) cc_final: 0.7732 (m-10) REVERT: S 227 PHE cc_start: 0.7233 (m-80) cc_final: 0.6918 (m-80) outliers start: 54 outliers final: 39 residues processed: 324 average time/residue: 0.1008 time to fit residues: 44.2732 Evaluate side-chains 343 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 296 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 211 PHE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 53 optimal weight: 0.0170 chunk 67 optimal weight: 0.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 230 ASN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 155 ASN B 239 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.156779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127951 restraints weight = 15446.931| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.73 r_work: 0.3514 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9157 Z= 0.151 Angle : 0.615 13.344 12396 Z= 0.319 Chirality : 0.043 0.325 1414 Planarity : 0.004 0.052 1554 Dihedral : 4.677 29.197 1227 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.06 % Allowed : 26.92 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.66 (0.25), residues: 1125 helix: 1.78 (0.26), residues: 407 sheet: -0.05 (0.29), residues: 284 loop : -0.42 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.023 0.002 TYR R 300 PHE 0.023 0.002 PHE S 227 TRP 0.030 0.001 TRP R 251 HIS 0.004 0.001 HIS R 310 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9154) covalent geometry : angle 0.61491 (12390) SS BOND : bond 0.00213 ( 3) SS BOND : angle 0.51688 ( 6) hydrogen bonds : bond 0.04355 ( 487) hydrogen bonds : angle 5.18161 ( 1398) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 284 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 PHE cc_start: 0.7492 (m-80) cc_final: 0.6893 (m-80) REVERT: R 121 MET cc_start: 0.7479 (mmt) cc_final: 0.6712 (mmt) REVERT: R 149 MET cc_start: 0.7381 (tpt) cc_final: 0.7110 (tpt) REVERT: R 159 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6894 (mp) REVERT: R 207 LEU cc_start: 0.5318 (OUTLIER) cc_final: 0.4899 (tt) REVERT: R 211 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6477 (m-80) REVERT: R 220 LYS cc_start: 0.8205 (mmmm) cc_final: 0.7773 (mmmm) REVERT: R 249 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6511 (mm) REVERT: R 306 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7008 (pttm) REVERT: A 197 LYS cc_start: 0.7406 (mtmt) cc_final: 0.6996 (mtmt) REVERT: A 270 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7906 (mmtm) REVERT: A 277 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7041 (tttt) REVERT: A 321 THR cc_start: 0.8332 (m) cc_final: 0.8013 (t) REVERT: A 332 VAL cc_start: 0.8055 (m) cc_final: 0.7780 (p) REVERT: A 349 LYS cc_start: 0.7843 (mtmt) cc_final: 0.7529 (ttmt) REVERT: B 52 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7245 (mmm-85) REVERT: B 130 GLU cc_start: 0.7961 (mp0) cc_final: 0.7608 (mp0) REVERT: B 134 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7480 (mtm-85) REVERT: B 163 ASP cc_start: 0.6790 (p0) cc_final: 0.6548 (p0) REVERT: B 175 GLN cc_start: 0.7160 (mm-40) cc_final: 0.6875 (mm-40) REVERT: B 183 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.7293 (t-170) REVERT: S 38 ARG cc_start: 0.7497 (ptt180) cc_final: 0.7213 (ptt180) REVERT: S 90 ASP cc_start: 0.7330 (m-30) cc_final: 0.7068 (m-30) REVERT: S 215 TYR cc_start: 0.7956 (m-10) cc_final: 0.7660 (m-10) REVERT: S 227 PHE cc_start: 0.7116 (m-80) cc_final: 0.6822 (m-80) outliers start: 50 outliers final: 35 residues processed: 310 average time/residue: 0.1120 time to fit residues: 46.5857 Evaluate side-chains 325 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 281 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 211 PHE Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 97 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 52 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.154871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126202 restraints weight = 15354.567| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.69 r_work: 0.3487 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9157 Z= 0.251 Angle : 0.667 14.129 12396 Z= 0.351 Chirality : 0.046 0.297 1414 Planarity : 0.004 0.060 1554 Dihedral : 4.870 28.643 1227 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.66 % Allowed : 26.92 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.46 (0.25), residues: 1125 helix: 1.61 (0.26), residues: 406 sheet: -0.23 (0.29), residues: 287 loop : -0.48 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 19 TYR 0.024 0.002 TYR R 300 PHE 0.032 0.002 PHE A 336 TRP 0.038 0.002 TRP R 251 HIS 0.003 0.001 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 9154) covalent geometry : angle 0.66721 (12390) SS BOND : bond 0.00250 ( 3) SS BOND : angle 0.55937 ( 6) hydrogen bonds : bond 0.04747 ( 487) hydrogen bonds : angle 5.35691 ( 1398) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 294 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7510 (m-10) REVERT: R 86 PHE cc_start: 0.7647 (m-80) cc_final: 0.6970 (m-80) REVERT: R 118 TYR cc_start: 0.7132 (m-80) cc_final: 0.6624 (m-80) REVERT: R 121 MET cc_start: 0.7463 (mmt) cc_final: 0.6720 (mmt) REVERT: R 149 MET cc_start: 0.7348 (tpt) cc_final: 0.7056 (tpt) REVERT: R 159 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6891 (mp) REVERT: R 207 LEU cc_start: 0.5556 (OUTLIER) cc_final: 0.5107 (tt) REVERT: R 211 PHE cc_start: 0.6985 (OUTLIER) cc_final: 0.6506 (m-80) REVERT: R 220 LYS cc_start: 0.8249 (mmmm) cc_final: 0.7843 (mmmm) REVERT: R 249 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6606 (mm) REVERT: R 251 TRP cc_start: 0.6699 (m100) cc_final: 0.6446 (m100) REVERT: R 306 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7048 (pttm) REVERT: A 197 LYS cc_start: 0.7501 (mtmt) cc_final: 0.7075 (mtmt) REVERT: A 270 LYS cc_start: 0.8215 (mmtm) cc_final: 0.7971 (mmtm) REVERT: A 277 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7188 (tttt) REVERT: A 321 THR cc_start: 0.8410 (m) cc_final: 0.8091 (t) REVERT: A 349 LYS cc_start: 0.7864 (mtmt) cc_final: 0.7554 (ttmt) REVERT: B 52 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7294 (mmm-85) REVERT: B 130 GLU cc_start: 0.7939 (mp0) cc_final: 0.7548 (mp0) REVERT: B 143 THR cc_start: 0.8346 (p) cc_final: 0.7953 (p) REVERT: B 175 GLN cc_start: 0.7246 (mm-40) cc_final: 0.6908 (mm-40) REVERT: B 183 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7384 (t-170) REVERT: S 38 ARG cc_start: 0.7680 (ptt180) cc_final: 0.7444 (ptt180) REVERT: S 90 ASP cc_start: 0.7256 (m-30) cc_final: 0.7025 (m-30) REVERT: S 206 ARG cc_start: 0.7444 (mtm110) cc_final: 0.7226 (mtm110) REVERT: S 215 TYR cc_start: 0.7978 (m-10) cc_final: 0.7684 (m-10) outliers start: 46 outliers final: 34 residues processed: 317 average time/residue: 0.1074 time to fit residues: 45.8248 Evaluate side-chains 335 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 292 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 211 PHE Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 141 GLU Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 18 optimal weight: 0.2980 chunk 14 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 155 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.156901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.128301 restraints weight = 15227.045| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.71 r_work: 0.3518 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9157 Z= 0.141 Angle : 0.627 13.705 12396 Z= 0.324 Chirality : 0.044 0.346 1414 Planarity : 0.004 0.055 1554 Dihedral : 4.652 29.472 1227 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.45 % Allowed : 27.23 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.58 (0.25), residues: 1125 helix: 1.74 (0.26), residues: 401 sheet: -0.06 (0.30), residues: 282 loop : -0.50 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.019 0.001 TYR R 300 PHE 0.026 0.002 PHE A 336 TRP 0.033 0.002 TRP R 251 HIS 0.004 0.001 HIS R 310 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9154) covalent geometry : angle 0.62674 (12390) SS BOND : bond 0.00231 ( 3) SS BOND : angle 0.43726 ( 6) hydrogen bonds : bond 0.04243 ( 487) hydrogen bonds : angle 5.15411 ( 1398) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 285 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 TYR cc_start: 0.7912 (OUTLIER) cc_final: 0.7461 (m-10) REVERT: R 86 PHE cc_start: 0.7535 (m-80) cc_final: 0.6922 (m-80) REVERT: R 118 TYR cc_start: 0.7094 (m-80) cc_final: 0.6529 (m-80) REVERT: R 121 MET cc_start: 0.7458 (mmt) cc_final: 0.6848 (mmt) REVERT: R 149 MET cc_start: 0.7376 (tpt) cc_final: 0.7086 (tpt) REVERT: R 159 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6918 (mp) REVERT: R 207 LEU cc_start: 0.5482 (OUTLIER) cc_final: 0.5039 (tt) REVERT: R 211 PHE cc_start: 0.6932 (OUTLIER) cc_final: 0.6460 (m-80) REVERT: R 249 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6444 (mm) REVERT: R 306 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.6963 (tttt) REVERT: A 197 LYS cc_start: 0.7470 (mtmt) cc_final: 0.7056 (mtmt) REVERT: A 270 LYS cc_start: 0.8110 (mmtm) cc_final: 0.7784 (mmtm) REVERT: A 277 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7231 (tttt) REVERT: A 321 THR cc_start: 0.8343 (m) cc_final: 0.8030 (t) REVERT: A 332 VAL cc_start: 0.8042 (m) cc_final: 0.7788 (p) REVERT: A 349 LYS cc_start: 0.7844 (mtmt) cc_final: 0.7523 (ttmt) REVERT: B 29 THR cc_start: 0.7929 (t) cc_final: 0.7469 (p) REVERT: B 52 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7252 (mmm-85) REVERT: B 75 GLN cc_start: 0.8210 (mm110) cc_final: 0.7849 (mm110) REVERT: B 130 GLU cc_start: 0.7955 (mp0) cc_final: 0.7594 (mp0) REVERT: B 175 GLN cc_start: 0.7207 (mm-40) cc_final: 0.6871 (mm-40) REVERT: B 183 HIS cc_start: 0.8159 (OUTLIER) cc_final: 0.7429 (t-170) REVERT: S 38 ARG cc_start: 0.7546 (ptt180) cc_final: 0.7272 (ptt180) REVERT: S 90 ASP cc_start: 0.7245 (m-30) cc_final: 0.6992 (m-30) REVERT: S 215 TYR cc_start: 0.7938 (m-10) cc_final: 0.7655 (m-10) REVERT: S 227 PHE cc_start: 0.7142 (m-80) cc_final: 0.6872 (m-80) outliers start: 44 outliers final: 29 residues processed: 306 average time/residue: 0.1102 time to fit residues: 45.1229 Evaluate side-chains 316 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 278 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 211 PHE Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.156219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127701 restraints weight = 15291.244| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.68 r_work: 0.3520 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 9157 Z= 0.229 Angle : 0.920 59.200 12396 Z= 0.528 Chirality : 0.046 0.360 1414 Planarity : 0.004 0.066 1554 Dihedral : 4.744 29.548 1227 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.05 % Allowed : 28.04 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.56 (0.25), residues: 1125 helix: 1.72 (0.26), residues: 401 sheet: -0.05 (0.30), residues: 282 loop : -0.52 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 48 TYR 0.018 0.002 TYR R 300 PHE 0.025 0.002 PHE A 336 TRP 0.032 0.002 TRP R 251 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 9154) covalent geometry : angle 0.91994 (12390) SS BOND : bond 0.00285 ( 3) SS BOND : angle 0.47993 ( 6) hydrogen bonds : bond 0.04297 ( 487) hydrogen bonds : angle 5.16081 ( 1398) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7447 (m-10) REVERT: R 86 PHE cc_start: 0.7500 (m-80) cc_final: 0.6917 (m-80) REVERT: R 118 TYR cc_start: 0.7068 (m-80) cc_final: 0.6532 (m-80) REVERT: R 121 MET cc_start: 0.7504 (mmt) cc_final: 0.6867 (mmt) REVERT: R 149 MET cc_start: 0.7391 (tpt) cc_final: 0.7113 (tpt) REVERT: R 159 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6934 (mp) REVERT: R 207 LEU cc_start: 0.5486 (OUTLIER) cc_final: 0.5028 (tt) REVERT: R 211 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.6498 (m-80) REVERT: R 249 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6449 (mm) REVERT: R 306 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.6976 (tttt) REVERT: A 197 LYS cc_start: 0.7471 (mtmt) cc_final: 0.7065 (mtmt) REVERT: A 270 LYS cc_start: 0.8119 (mmtm) cc_final: 0.7812 (mmtm) REVERT: A 277 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7206 (tttt) REVERT: A 321 THR cc_start: 0.8336 (m) cc_final: 0.8038 (t) REVERT: A 332 VAL cc_start: 0.8046 (m) cc_final: 0.7794 (p) REVERT: A 349 LYS cc_start: 0.7847 (mtmt) cc_final: 0.7523 (ttmt) REVERT: B 29 THR cc_start: 0.7933 (t) cc_final: 0.7469 (p) REVERT: B 52 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7276 (mmm-85) REVERT: B 75 GLN cc_start: 0.8204 (mm110) cc_final: 0.7850 (mm110) REVERT: B 130 GLU cc_start: 0.7904 (mp0) cc_final: 0.7476 (mp0) REVERT: B 175 GLN cc_start: 0.7220 (mm-40) cc_final: 0.6892 (mm-40) REVERT: B 183 HIS cc_start: 0.8174 (OUTLIER) cc_final: 0.7446 (t-170) REVERT: S 38 ARG cc_start: 0.7553 (ptt180) cc_final: 0.7276 (ptt180) REVERT: S 90 ASP cc_start: 0.7243 (m-30) cc_final: 0.6994 (m-30) REVERT: S 215 TYR cc_start: 0.7948 (m-10) cc_final: 0.7663 (m-10) REVERT: S 227 PHE cc_start: 0.7158 (m-80) cc_final: 0.6879 (m-80) outliers start: 40 outliers final: 29 residues processed: 299 average time/residue: 0.1088 time to fit residues: 43.7734 Evaluate side-chains 317 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 279 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 211 PHE Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 68 optimal weight: 0.0270 chunk 90 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 75 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.156476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.128104 restraints weight = 15108.790| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.68 r_work: 0.3522 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 9157 Z= 0.229 Angle : 0.920 59.200 12396 Z= 0.528 Chirality : 0.046 0.360 1414 Planarity : 0.004 0.066 1554 Dihedral : 4.744 29.548 1227 Min Nonbonded Distance : 1.294 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.85 % Allowed : 28.24 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.56 (0.25), residues: 1125 helix: 1.72 (0.26), residues: 401 sheet: -0.05 (0.30), residues: 282 loop : -0.52 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 48 TYR 0.018 0.002 TYR R 300 PHE 0.025 0.002 PHE A 336 TRP 0.032 0.002 TRP R 251 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 9154) covalent geometry : angle 0.91994 (12390) SS BOND : bond 0.00285 ( 3) SS BOND : angle 0.47993 ( 6) hydrogen bonds : bond 0.04297 ( 487) hydrogen bonds : angle 5.16081 ( 1398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2330.57 seconds wall clock time: 40 minutes 56.86 seconds (2456.86 seconds total)