Starting phenix.real_space_refine on Thu Jul 2 13:40:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vif_32007/07_2026/7vif_32007.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vif_32007/07_2026/7vif_32007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vif_32007/07_2026/7vif_32007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vif_32007/07_2026/7vif_32007.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vif_32007/07_2026/7vif_32007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vif_32007/07_2026/7vif_32007.map" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.052 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 65 5.16 5 C 5689 2.51 5 N 1507 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8918 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1804 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Chain: "F" Number of atoms: 2245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2245 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 6, 'TRANS': 273} Chain breaks: 2 Chain: "D" Number of atoms: 1806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1800 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 225, 1800 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 1822 Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'J89': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS D 305 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 305 " occ=0.50 Time building chain proxies: 2.12, per 1000 atoms: 0.24 Number of scatterers: 8918 At special positions: 0 Unit cell: (88.81, 118.69, 129.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 P 1 15.00 O 1656 8.00 N 1507 7.00 C 5689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS F 184 " - pdb=" SG CYS F 191 " distance=2.03 Simple disulfide: pdb=" SG CYS F 282 " - pdb=" SG CYS F 287 " 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: 0.69 Conformation dependent library (CDL) restraints added in 592.0 milliseconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 38.9% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 2 through 24 Processing helix chain 'A' and resid 28 through 33 Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.985A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.008A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.615A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 31 Processing helix chain 'F' and resid 49 through 73 Processing helix chain 'F' and resid 74 through 77 Processing helix chain 'F' and resid 78 through 105 Processing helix chain 'F' and resid 106 through 111 Processing helix chain 'F' and resid 113 through 148 removed outlier: 3.602A pdb=" N MET F 124 " --> pdb=" O ARG F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 177 removed outlier: 3.643A pdb=" N SER F 171 " --> pdb=" O CYS F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 181 removed outlier: 3.525A pdb=" N GLY F 181 " --> pdb=" O PRO F 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 178 through 181' Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'F' and resid 199 through 235 removed outlier: 3.732A pdb=" N LEU F 235 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 282 Proline residue: F 271 - end of helix removed outlier: 4.391A pdb=" N VAL F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY F 281 " --> pdb=" O LEU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 314 removed outlier: 3.771A pdb=" N ALA F 300 " --> pdb=" O PHE F 296 " (cutoff:3.500A) Proline residue: F 308 - end of helix Processing helix chain 'F' and resid 315 through 324 Processing helix chain 'D' and resid 6 through 32 removed outlier: 3.549A pdb=" N ARG D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 56 Processing helix chain 'D' and resid 207 through 216 removed outlier: 3.773A pdb=" N LYS D 210 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE D 212 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N HIS D 213 " --> pdb=" O LYS D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 removed outlier: 3.843A pdb=" N ASP D 231 " --> pdb=" O SER D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 255 Processing helix chain 'D' and resid 270 through 278 removed outlier: 3.732A pdb=" N GLU D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 286 Processing helix chain 'D' and resid 295 through 310 removed outlier: 3.558A pdb=" N LEU D 310 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 351 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50 removed outlier: 5.581A pdb=" N THR A 46 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASN A 339 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 48 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 61 removed outlier: 3.647A pdb=" N ALA A 59 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 78 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA A 91 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A 80 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 104 removed outlier: 6.018A pdb=" N ASN A 124 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL A 134 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 150 removed outlier: 3.883A pdb=" N THR A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP A 169 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN A 175 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 191 removed outlier: 6.574A pdb=" N ALA A 207 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR A 220 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU A 209 " --> pdb=" O ARG A 218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 233 removed outlier: 6.633A pdb=" N CYS A 249 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR A 262 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU A 251 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 277 removed outlier: 3.722A pdb=" N SER A 274 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N CYS A 293 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL A 306 " --> pdb=" O CYS A 293 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 295 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.765A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.109A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.554A pdb=" N THR E 213 " --> pdb=" O SER E 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 149 removed outlier: 6.391A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 185 through 191 removed outlier: 6.450A pdb=" N ILE D 221 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N PHE D 267 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE D 223 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ASN D 269 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 225 " --> pdb=" O ASN D 269 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1327 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: 1.66 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1432 1.30 - 1.43: 2393 1.43 - 1.56: 5171 1.56 - 1.69: 6 1.69 - 1.82: 92 Bond restraints: 9094 Sorted by residual: bond pdb=" CA TYR F 98 " pdb=" C TYR F 98 " ideal model delta sigma weight residual 1.523 1.439 0.084 1.35e-02 5.49e+03 3.90e+01 bond pdb=" C GLY F 106 " pdb=" O GLY F 106 " ideal model delta sigma weight residual 1.234 1.165 0.069 1.17e-02 7.31e+03 3.50e+01 bond pdb=" C ALA F 100 " pdb=" O ALA F 100 " ideal model delta sigma weight residual 1.237 1.171 0.066 1.16e-02 7.43e+03 3.20e+01 bond pdb=" CA ALA F 100 " pdb=" C ALA F 100 " ideal model delta sigma weight residual 1.524 1.457 0.067 1.26e-02 6.30e+03 2.83e+01 bond pdb=" CA ASN F 101 " pdb=" C ASN F 101 " ideal model delta sigma weight residual 1.523 1.457 0.066 1.30e-02 5.92e+03 2.57e+01 ... (remaining 9089 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 12161 2.36 - 4.72: 112 4.72 - 7.08: 22 7.08 - 9.45: 7 9.45 - 11.81: 3 Bond angle restraints: 12305 Sorted by residual: angle pdb=" N LEU F 104 " pdb=" CA LEU F 104 " pdb=" C LEU F 104 " ideal model delta sigma weight residual 111.28 119.17 -7.89 1.09e+00 8.42e-01 5.24e+01 angle pdb=" C LEU F 103 " pdb=" N LEU F 104 " pdb=" CA LEU F 104 " ideal model delta sigma weight residual 120.28 128.86 -8.58 1.34e+00 5.57e-01 4.10e+01 angle pdb=" N GLY F 106 " pdb=" CA GLY F 106 " pdb=" C GLY F 106 " ideal model delta sigma weight residual 111.76 103.49 8.27 1.43e+00 4.89e-01 3.35e+01 angle pdb=" N LEU F 103 " pdb=" CA LEU F 103 " pdb=" C LEU F 103 " ideal model delta sigma weight residual 111.36 116.47 -5.11 1.09e+00 8.42e-01 2.20e+01 angle pdb=" CA ASN F 101 " pdb=" C ASN F 101 " pdb=" N LEU F 102 " ideal model delta sigma weight residual 117.30 112.72 4.58 1.16e+00 7.43e-01 1.56e+01 ... (remaining 12300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.07: 5218 27.07 - 54.13: 186 54.13 - 81.20: 15 81.20 - 108.27: 0 108.27 - 135.33: 1 Dihedral angle restraints: 5420 sinusoidal: 2125 harmonic: 3295 Sorted by residual: dihedral pdb=" CA GLU D 207 " pdb=" C GLU D 207 " pdb=" N ARG D 208 " pdb=" CA ARG D 208 " ideal model delta harmonic sigma weight residual 180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA GLU E 234 " pdb=" C GLU E 234 " pdb=" N TYR E 235 " pdb=" CA TYR E 235 " ideal model delta harmonic sigma weight residual -180.00 -157.52 -22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" C16 J89 F 401 " pdb=" C17 J89 F 401 " pdb=" C18 J89 F 401 " pdb=" O19 J89 F 401 " ideal model delta sinusoidal sigma weight residual -52.49 82.84 -135.33 1 3.00e+01 1.11e-03 1.83e+01 ... (remaining 5417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1188 0.057 - 0.114: 191 0.114 - 0.171: 28 0.171 - 0.227: 3 0.227 - 0.284: 2 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA LEU F 102 " pdb=" N LEU F 102 " pdb=" C LEU F 102 " pdb=" CB LEU F 102 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA LEU F 103 " pdb=" N LEU F 103 " pdb=" C LEU F 103 " pdb=" CB LEU F 103 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA TYR F 98 " pdb=" N TYR F 98 " pdb=" C TYR F 98 " pdb=" CB TYR F 98 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1409 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 105 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C SER F 105 " -0.047 2.00e-02 2.50e+03 pdb=" O SER F 105 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY F 106 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO E 236 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 113 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO F 114 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO F 114 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 114 " -0.028 5.00e-02 4.00e+02 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1459 2.76 - 3.30: 8541 3.30 - 3.83: 15089 3.83 - 4.37: 18356 4.37 - 4.90: 32002 Nonbonded interactions: 75447 Sorted by model distance: nonbonded pdb=" O ILE A 57 " pdb=" OG SER A 315 " model vdw 2.229 3.040 nonbonded pdb=" O LEU F 174 " pdb=" OH TYR F 202 " model vdw 2.236 3.040 nonbonded pdb=" NH1 ARG A 41 " pdb=" O ILE A 42 " model vdw 2.242 3.120 nonbonded pdb=" O GLN A 74 " pdb=" OG SER A 97 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR D 290 " pdb=" O SER D 293 " model vdw 2.263 3.040 ... (remaining 75442 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.990 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 0.084 9098 Z= 0.264 Angle : 0.636 11.807 12313 Z= 0.338 Chirality : 0.044 0.284 1412 Planarity : 0.004 0.053 1537 Dihedral : 13.158 135.331 3282 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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 are not related in a simple way. whole: 1.08 (0.25), residues: 1118 helix: 2.12 (0.25), residues: 393 sheet: 0.39 (0.30), residues: 283 loop : -0.29 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 319 TYR 0.027 0.002 TYR F 98 PHE 0.011 0.001 PHE F 58 TRP 0.030 0.001 TRP F 117 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.26 ( 9094) covalent geometry : angle 0.63634 / 0.34 (12305) SS BOND : bond 0.00213 / 0.11 ( 4) SS BOND : angle 0.73222 / 0.31 ( 8) hydrogen bonds : bond 0.13669 / 9.41 ( 473) hydrogen bonds : angle 5.59283 / 3.99 ( 1327) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.404 Fit side-chains REVERT: A 14 LYS cc_start: 0.7540 (mttm) cc_final: 0.7339 (mptt) REVERT: A 45 ARG cc_start: 0.7101 (mmt-90) cc_final: 0.6879 (mtm-85) REVERT: E 230 MET cc_start: 0.8474 (ttp) cc_final: 0.8269 (ttt) REVERT: F 316 LYS cc_start: 0.7745 (mmmt) cc_final: 0.6768 (mtmm) REVERT: F 318 MET cc_start: 0.7791 (tpp) cc_final: 0.7443 (tpt) REVERT: D 330 LYS cc_start: 0.8195 (mtmm) cc_final: 0.7384 (tmtt) outliers start: 0 outliers final: 1 residues processed: 177 average time/residue: 0.6177 time to fit residues: 116.1086 Evaluate side-chains 128 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 173 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.1980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN A 267 ASN E 77 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 ASN F 303 ASN ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.148006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117551 restraints weight = 19015.208| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.26 r_work: 0.3188 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9098 Z= 0.168 Angle : 0.559 6.885 12313 Z= 0.296 Chirality : 0.042 0.216 1412 Planarity : 0.005 0.063 1537 Dihedral : 6.971 151.623 1254 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.54 % Allowed : 11.49 % Favored : 86.97 % 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 are not related in a simple way. whole: 1.17 (0.25), residues: 1118 helix: 2.21 (0.25), residues: 396 sheet: 0.56 (0.31), residues: 272 loop : -0.35 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 319 TYR 0.031 0.002 TYR E 235 PHE 0.030 0.002 PHE F 58 TRP 0.014 0.001 TRP A 168 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 9094) covalent geometry : angle 0.55867 / 0.30 (12305) SS BOND : bond 0.00296 / 0.14 ( 4) SS BOND : angle 0.96395 / 0.43 ( 8) hydrogen bonds : bond 0.03774 / 2.48 ( 473) hydrogen bonds : angle 4.49849 / 3.18 ( 1327) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.340 Fit side-chains REVERT: A 14 LYS cc_start: 0.7951 (mttm) cc_final: 0.7678 (ttpt) REVERT: A 242 THR cc_start: 0.9071 (p) cc_final: 0.8852 (p) REVERT: E 18 ARG cc_start: 0.8651 (mmt-90) cc_final: 0.8451 (tpt170) REVERT: F 307 ASN cc_start: 0.7542 (m110) cc_final: 0.6944 (m110) REVERT: D 240 MET cc_start: 0.6592 (pmm) cc_final: 0.6311 (pmm) REVERT: D 275 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7168 (tp30) REVERT: D 330 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8199 (mttm) outliers start: 15 outliers final: 5 residues processed: 141 average time/residue: 0.5687 time to fit residues: 85.2969 Evaluate side-chains 123 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 275 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 39 optimal weight: 0.0000 chunk 53 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN F 63 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 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 = 0.3712 r_free = 0.3712 target = 0.147384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116786 restraints weight = 23714.559| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.85 r_work: 0.3157 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9098 Z= 0.161 Angle : 0.526 6.907 12313 Z= 0.282 Chirality : 0.042 0.232 1412 Planarity : 0.005 0.056 1537 Dihedral : 6.909 153.784 1254 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.26 % Allowed : 13.44 % Favored : 84.31 % 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 are not related in a simple way. whole: 1.09 (0.25), residues: 1118 helix: 2.15 (0.25), residues: 396 sheet: 0.46 (0.30), residues: 278 loop : -0.36 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 233 TYR 0.037 0.002 TYR E 235 PHE 0.025 0.001 PHE F 58 TRP 0.017 0.001 TRP F 117 HIS 0.003 0.001 HIS F 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 9094) covalent geometry : angle 0.52581 / 0.28 (12305) SS BOND : bond 0.00248 / 0.12 ( 4) SS BOND : angle 0.92322 / 0.42 ( 8) hydrogen bonds : bond 0.03681 / 2.41 ( 473) hydrogen bonds : angle 4.31720 / 3.06 ( 1327) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.361 Fit side-chains REVERT: A 14 LYS cc_start: 0.7956 (mttm) cc_final: 0.7669 (ttpt) REVERT: A 100 MET cc_start: 0.9016 (mtm) cc_final: 0.8816 (mtm) REVERT: C 22 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7283 (mt-10) REVERT: E 18 ARG cc_start: 0.8688 (mmt-90) cc_final: 0.8393 (tpt170) REVERT: E 43 LYS cc_start: 0.8676 (mmtm) cc_final: 0.8470 (mptt) REVERT: E 76 LYS cc_start: 0.8614 (mmtm) cc_final: 0.8177 (mmtm) REVERT: E 158 SER cc_start: 0.8861 (t) cc_final: 0.8578 (m) REVERT: F 170 ILE cc_start: 0.7830 (mp) cc_final: 0.7518 (tt) REVERT: F 173 ILE cc_start: 0.7197 (mp) cc_final: 0.6910 (mp) REVERT: F 307 ASN cc_start: 0.7679 (m110) cc_final: 0.6891 (m110) REVERT: F 318 MET cc_start: 0.7734 (tpt) cc_final: 0.7414 (tpt) REVERT: D 240 MET cc_start: 0.6648 (pmm) cc_final: 0.6373 (pmm) REVERT: D 330 LYS cc_start: 0.8594 (mtmm) cc_final: 0.8232 (mttm) outliers start: 22 outliers final: 7 residues processed: 132 average time/residue: 0.5649 time to fit residues: 79.5173 Evaluate side-chains 120 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 229 ARG Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain D residue 225 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.0670 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN F 63 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 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 = 0.3719 r_free = 0.3719 target = 0.148105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118620 restraints weight = 22078.124| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.64 r_work: 0.3181 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9098 Z= 0.131 Angle : 0.495 6.808 12313 Z= 0.266 Chirality : 0.041 0.216 1412 Planarity : 0.004 0.056 1537 Dihedral : 6.582 150.022 1252 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.46 % Allowed : 14.26 % Favored : 83.28 % 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 are not related in a simple way. whole: 1.21 (0.25), residues: 1118 helix: 2.28 (0.25), residues: 396 sheet: 0.49 (0.30), residues: 283 loop : -0.31 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 233 TYR 0.035 0.002 TYR E 235 PHE 0.024 0.001 PHE F 58 TRP 0.023 0.001 TRP F 117 HIS 0.003 0.001 HIS F 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9094) covalent geometry : angle 0.49469 / 0.27 (12305) SS BOND : bond 0.00236 / 0.12 ( 4) SS BOND : angle 0.76598 / 0.34 ( 8) hydrogen bonds : bond 0.03383 / 2.21 ( 473) hydrogen bonds : angle 4.17368 / 2.95 ( 1327) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.350 Fit side-chains REVERT: A 14 LYS cc_start: 0.7891 (mttm) cc_final: 0.7569 (ttpt) REVERT: C 22 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7143 (mt-10) REVERT: E 18 ARG cc_start: 0.8592 (mmt-90) cc_final: 0.8295 (tpt170) REVERT: E 43 LYS cc_start: 0.8626 (mmtm) cc_final: 0.8365 (mptt) REVERT: E 158 SER cc_start: 0.8829 (t) cc_final: 0.8571 (m) REVERT: F 63 ASN cc_start: 0.7656 (m-40) cc_final: 0.7417 (m110) REVERT: F 307 ASN cc_start: 0.7516 (m110) cc_final: 0.6680 (m110) REVERT: D 240 MET cc_start: 0.6576 (pmm) cc_final: 0.6292 (pmm) REVERT: D 330 LYS cc_start: 0.8483 (mtmm) cc_final: 0.8067 (mttm) outliers start: 24 outliers final: 9 residues processed: 146 average time/residue: 0.5175 time to fit residues: 81.1284 Evaluate side-chains 127 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain D residue 225 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.148297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118373 restraints weight = 25001.590| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.00 r_work: 0.3160 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9098 Z= 0.130 Angle : 0.500 6.621 12313 Z= 0.267 Chirality : 0.041 0.219 1412 Planarity : 0.004 0.056 1537 Dihedral : 7.064 169.670 1252 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.46 % Allowed : 15.79 % Favored : 81.74 % 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 are not related in a simple way. whole: 1.28 (0.25), residues: 1118 helix: 2.33 (0.25), residues: 396 sheet: 0.50 (0.30), residues: 283 loop : -0.25 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 233 TYR 0.036 0.002 TYR E 235 PHE 0.027 0.001 PHE F 58 TRP 0.026 0.001 TRP F 117 HIS 0.002 0.001 HIS F 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 9094) covalent geometry : angle 0.50013 / 0.27 (12305) SS BOND : bond 0.00226 / 0.11 ( 4) SS BOND : angle 0.76732 / 0.35 ( 8) hydrogen bonds : bond 0.03399 / 2.23 ( 473) hydrogen bonds : angle 4.15555 / 2.94 ( 1327) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.218 Fit side-chains REVERT: A 14 LYS cc_start: 0.7967 (mttm) cc_final: 0.7678 (ttpt) REVERT: A 77 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.7650 (mptt) REVERT: A 216 MET cc_start: 0.9227 (pmm) cc_final: 0.8968 (pmm) REVERT: A 258 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.7167 (pm20) REVERT: C 22 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7219 (mt-10) REVERT: E 18 ARG cc_start: 0.8632 (mmt-90) cc_final: 0.8346 (tpt170) REVERT: E 76 LYS cc_start: 0.8264 (mmtm) cc_final: 0.8042 (mtmt) REVERT: E 158 SER cc_start: 0.8830 (t) cc_final: 0.8586 (m) REVERT: F 63 ASN cc_start: 0.7851 (m-40) cc_final: 0.7609 (m110) REVERT: F 173 ILE cc_start: 0.7152 (mp) cc_final: 0.6819 (mp) REVERT: F 266 ILE cc_start: 0.7426 (mp) cc_final: 0.7033 (mt) REVERT: F 273 PHE cc_start: 0.7517 (t80) cc_final: 0.7316 (t80) REVERT: F 318 MET cc_start: 0.8012 (tpp) cc_final: 0.7763 (tpt) REVERT: D 240 MET cc_start: 0.6620 (pmm) cc_final: 0.6372 (pmm) REVERT: D 330 LYS cc_start: 0.8579 (mtmm) cc_final: 0.8209 (mttm) outliers start: 24 outliers final: 7 residues processed: 142 average time/residue: 0.4527 time to fit residues: 69.0007 Evaluate side-chains 130 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 252 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 64 optimal weight: 0.0980 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN D 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.146945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117132 restraints weight = 20226.055| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.38 r_work: 0.3174 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9098 Z= 0.159 Angle : 0.518 6.521 12313 Z= 0.277 Chirality : 0.042 0.221 1412 Planarity : 0.005 0.056 1537 Dihedral : 7.376 178.024 1252 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.56 % Allowed : 16.21 % Favored : 81.23 % 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 are not related in a simple way. whole: 1.18 (0.25), residues: 1118 helix: 2.29 (0.25), residues: 396 sheet: 0.40 (0.30), residues: 285 loop : -0.31 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 233 TYR 0.036 0.002 TYR E 235 PHE 0.025 0.001 PHE F 58 TRP 0.027 0.001 TRP F 117 HIS 0.003 0.001 HIS F 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 9094) covalent geometry : angle 0.51763 / 0.28 (12305) SS BOND : bond 0.00285 / 0.14 ( 4) SS BOND : angle 0.84799 / 0.39 ( 8) hydrogen bonds : bond 0.03525 / 2.30 ( 473) hydrogen bonds : angle 4.20759 / 2.99 ( 1327) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.367 Fit side-chains REVERT: A 14 LYS cc_start: 0.7902 (mttm) cc_final: 0.7590 (ttpt) REVERT: A 77 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.7639 (mptt) REVERT: A 216 MET cc_start: 0.9159 (pmm) cc_final: 0.8798 (pmm) REVERT: A 258 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: C 22 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7194 (mt-10) REVERT: E 18 ARG cc_start: 0.8633 (mmt-90) cc_final: 0.8337 (tpt170) REVERT: E 43 LYS cc_start: 0.8812 (mptt) cc_final: 0.8589 (mmtm) REVERT: E 158 SER cc_start: 0.8834 (t) cc_final: 0.8558 (m) REVERT: F 63 ASN cc_start: 0.7751 (m-40) cc_final: 0.7450 (m110) REVERT: F 266 ILE cc_start: 0.7385 (mp) cc_final: 0.6965 (mt) REVERT: F 273 PHE cc_start: 0.7556 (t80) cc_final: 0.7275 (t80) REVERT: F 302 LEU cc_start: 0.7079 (mt) cc_final: 0.6768 (mt) REVERT: D 240 MET cc_start: 0.6532 (pmm) cc_final: 0.6278 (pmm) REVERT: D 330 LYS cc_start: 0.8524 (mtmm) cc_final: 0.8116 (mttm) outliers start: 25 outliers final: 11 residues processed: 146 average time/residue: 0.5551 time to fit residues: 86.8209 Evaluate side-chains 132 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 252 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN D 306 GLN ** D 347 ASN ** 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 = 0.3693 r_free = 0.3693 target = 0.146065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.116730 restraints weight = 22865.126| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.72 r_work: 0.3147 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9098 Z= 0.180 Angle : 0.541 7.115 12313 Z= 0.287 Chirality : 0.043 0.198 1412 Planarity : 0.005 0.056 1537 Dihedral : 7.383 177.353 1252 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.67 % Allowed : 16.62 % Favored : 80.72 % 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 are not related in a simple way. whole: 1.11 (0.25), residues: 1118 helix: 2.24 (0.25), residues: 396 sheet: 0.31 (0.30), residues: 287 loop : -0.32 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 233 TYR 0.025 0.002 TYR D 302 PHE 0.024 0.001 PHE F 58 TRP 0.029 0.002 TRP F 117 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 9094) covalent geometry : angle 0.54037 / 0.29 (12305) SS BOND : bond 0.00258 / 0.13 ( 4) SS BOND : angle 0.88510 / 0.41 ( 8) hydrogen bonds : bond 0.03638 / 2.37 ( 473) hydrogen bonds : angle 4.28022 / 3.04 ( 1327) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.373 Fit side-chains REVERT: A 14 LYS cc_start: 0.7904 (mttm) cc_final: 0.7560 (mtmm) REVERT: A 77 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.7677 (mptt) REVERT: A 216 MET cc_start: 0.9170 (pmm) cc_final: 0.8843 (pmm) REVERT: A 258 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.7220 (pm20) REVERT: C 22 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7208 (mt-10) REVERT: E 18 ARG cc_start: 0.8629 (mmt-90) cc_final: 0.8334 (tpt170) REVERT: E 76 LYS cc_start: 0.8457 (mmtm) cc_final: 0.8143 (mtmt) REVERT: E 158 SER cc_start: 0.8858 (t) cc_final: 0.8575 (m) REVERT: E 235 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7511 (t80) REVERT: F 63 ASN cc_start: 0.7754 (m-40) cc_final: 0.7443 (m110) REVERT: F 266 ILE cc_start: 0.7372 (mp) cc_final: 0.6959 (mt) REVERT: F 273 PHE cc_start: 0.7661 (t80) cc_final: 0.7373 (t80) REVERT: F 302 LEU cc_start: 0.7090 (mt) cc_final: 0.6798 (mt) REVERT: F 307 ASN cc_start: 0.7686 (m110) cc_final: 0.6902 (m-40) REVERT: D 240 MET cc_start: 0.6533 (pmm) cc_final: 0.6314 (pmm) REVERT: D 330 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8104 (mttm) outliers start: 26 outliers final: 15 residues processed: 146 average time/residue: 0.5159 time to fit residues: 81.0193 Evaluate side-chains 138 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 268 CYS Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 252 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN F 315 ASN ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN D 306 GLN ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.147914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118147 restraints weight = 18984.491| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.18 r_work: 0.3195 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9098 Z= 0.132 Angle : 0.507 6.315 12313 Z= 0.271 Chirality : 0.042 0.170 1412 Planarity : 0.005 0.056 1537 Dihedral : 6.352 151.753 1252 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.15 % Allowed : 17.74 % Favored : 80.10 % 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 are not related in a simple way. whole: 1.14 (0.26), residues: 1118 helix: 2.19 (0.25), residues: 403 sheet: 0.40 (0.30), residues: 285 loop : -0.33 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 233 TYR 0.021 0.001 TYR E 235 PHE 0.022 0.001 PHE F 58 TRP 0.032 0.001 TRP F 117 HIS 0.002 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 9094) covalent geometry : angle 0.50673 / 0.27 (12305) SS BOND : bond 0.00226 / 0.11 ( 4) SS BOND : angle 0.69948 / 0.32 ( 8) hydrogen bonds : bond 0.03353 / 2.19 ( 473) hydrogen bonds : angle 4.19727 / 2.98 ( 1327) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.348 Fit side-chains REVERT: A 14 LYS cc_start: 0.7912 (mttm) cc_final: 0.7576 (mtmm) REVERT: A 77 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.7625 (mptt) REVERT: A 216 MET cc_start: 0.9169 (pmm) cc_final: 0.8890 (pmm) REVERT: A 258 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.7149 (pm20) REVERT: C 22 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7205 (mt-10) REVERT: E 18 ARG cc_start: 0.8582 (mmt-90) cc_final: 0.8301 (tpt170) REVERT: E 76 LYS cc_start: 0.8250 (mmtm) cc_final: 0.8027 (mtmt) REVERT: E 87 ARG cc_start: 0.7676 (mtt90) cc_final: 0.7463 (mtm-85) REVERT: E 158 SER cc_start: 0.8806 (t) cc_final: 0.8550 (m) REVERT: E 235 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.7080 (t80) REVERT: F 58 PHE cc_start: 0.7788 (t80) cc_final: 0.7373 (t80) REVERT: F 63 ASN cc_start: 0.7578 (m-40) cc_final: 0.7357 (m110) REVERT: F 173 ILE cc_start: 0.7012 (mp) cc_final: 0.6685 (mp) REVERT: F 266 ILE cc_start: 0.7356 (mp) cc_final: 0.6947 (mt) REVERT: F 273 PHE cc_start: 0.7699 (t80) cc_final: 0.7441 (t80) REVERT: F 302 LEU cc_start: 0.7037 (mt) cc_final: 0.6740 (mt) REVERT: F 307 ASN cc_start: 0.7619 (m110) cc_final: 0.6861 (m110) REVERT: F 318 MET cc_start: 0.7856 (tpt) cc_final: 0.7405 (tpt) REVERT: D 240 MET cc_start: 0.6504 (pmm) cc_final: 0.6237 (pmm) REVERT: D 276 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8120 (pt0) REVERT: D 330 LYS cc_start: 0.8454 (mtmm) cc_final: 0.8037 (mttm) outliers start: 21 outliers final: 11 residues processed: 144 average time/residue: 0.5436 time to fit residues: 84.0813 Evaluate side-chains 141 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 276 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN D 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.148086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117763 restraints weight = 17525.593| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.07 r_work: 0.3195 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9098 Z= 0.133 Angle : 0.521 8.178 12313 Z= 0.276 Chirality : 0.042 0.163 1412 Planarity : 0.005 0.057 1537 Dihedral : 5.987 134.899 1252 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.36 % Allowed : 17.64 % Favored : 80.00 % 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 are not related in a simple way. whole: 1.12 (0.26), residues: 1118 helix: 2.17 (0.25), residues: 403 sheet: 0.42 (0.30), residues: 283 loop : -0.36 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 233 TYR 0.022 0.001 TYR E 235 PHE 0.029 0.001 PHE F 58 TRP 0.035 0.001 TRP F 117 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 9094) covalent geometry : angle 0.52089 / 0.28 (12305) SS BOND : bond 0.00208 / 0.10 ( 4) SS BOND : angle 0.72635 / 0.34 ( 8) hydrogen bonds : bond 0.03340 / 2.18 ( 473) hydrogen bonds : angle 4.17477 / 2.96 ( 1327) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.265 Fit side-chains REVERT: A 14 LYS cc_start: 0.7966 (mttm) cc_final: 0.7661 (mtmm) REVERT: A 77 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.7629 (mptt) REVERT: A 216 MET cc_start: 0.9173 (pmm) cc_final: 0.8913 (pmm) REVERT: A 258 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.7213 (pm20) REVERT: C 22 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7221 (mt-10) REVERT: E 18 ARG cc_start: 0.8611 (mmt-90) cc_final: 0.8331 (tpt170) REVERT: E 76 LYS cc_start: 0.8283 (mmtm) cc_final: 0.8066 (mtmt) REVERT: E 87 ARG cc_start: 0.7702 (mtt90) cc_final: 0.7494 (mtm-85) REVERT: E 158 SER cc_start: 0.8798 (t) cc_final: 0.8549 (m) REVERT: E 235 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.6961 (t80) REVERT: F 173 ILE cc_start: 0.7127 (mp) cc_final: 0.6801 (mp) REVERT: F 266 ILE cc_start: 0.7394 (mp) cc_final: 0.6990 (mt) REVERT: F 273 PHE cc_start: 0.7777 (t80) cc_final: 0.7557 (t80) REVERT: F 302 LEU cc_start: 0.7059 (mt) cc_final: 0.6782 (mt) REVERT: D 240 MET cc_start: 0.6439 (pmm) cc_final: 0.6217 (pmm) REVERT: D 330 LYS cc_start: 0.8478 (mtmm) cc_final: 0.8087 (mttm) outliers start: 23 outliers final: 11 residues processed: 140 average time/residue: 0.5701 time to fit residues: 85.5032 Evaluate side-chains 140 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 252 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 75 optimal weight: 0.0010 chunk 76 optimal weight: 0.0270 chunk 79 optimal weight: 0.6980 overall best weight: 0.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN D 256 ASN D 269 ASN D 306 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.150538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.120158 restraints weight = 13628.899| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.81 r_work: 0.3261 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9098 Z= 0.105 Angle : 0.494 7.838 12313 Z= 0.262 Chirality : 0.041 0.161 1412 Planarity : 0.005 0.056 1537 Dihedral : 5.564 122.343 1252 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.13 % Allowed : 19.08 % Favored : 79.79 % 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 are not related in a simple way. whole: 1.20 (0.26), residues: 1118 helix: 2.27 (0.26), residues: 403 sheet: 0.44 (0.31), residues: 277 loop : -0.32 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 233 TYR 0.022 0.001 TYR E 235 PHE 0.028 0.001 PHE F 58 TRP 0.036 0.001 TRP F 117 HIS 0.002 0.001 HIS D 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 9094) covalent geometry : angle 0.49419 / 0.26 (12305) SS BOND : bond 0.00181 / 0.09 ( 4) SS BOND : angle 0.55857 / 0.26 ( 8) hydrogen bonds : bond 0.03067 / 2.02 ( 473) hydrogen bonds : angle 4.07447 / 2.88 ( 1327) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.340 Fit side-chains REVERT: A 14 LYS cc_start: 0.7890 (mttm) cc_final: 0.7634 (ttpt) REVERT: A 77 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7626 (mptt) REVERT: A 216 MET cc_start: 0.9158 (pmm) cc_final: 0.8932 (pmm) REVERT: A 258 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.7098 (pm20) REVERT: C 22 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7128 (mt-10) REVERT: E 18 ARG cc_start: 0.8565 (mmt-90) cc_final: 0.8293 (tpt170) REVERT: E 43 LYS cc_start: 0.8791 (mptm) cc_final: 0.8468 (mmmt) REVERT: E 235 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.6594 (t80) REVERT: F 173 ILE cc_start: 0.7117 (mp) cc_final: 0.6838 (mp) REVERT: F 266 ILE cc_start: 0.7361 (mp) cc_final: 0.6960 (mt) REVERT: F 273 PHE cc_start: 0.7678 (t80) cc_final: 0.7465 (t80) REVERT: F 302 LEU cc_start: 0.7026 (mt) cc_final: 0.6750 (mt) REVERT: D 240 MET cc_start: 0.6332 (pmm) cc_final: 0.6119 (pmm) REVERT: D 330 LYS cc_start: 0.8405 (mtmm) cc_final: 0.8025 (mttm) outliers start: 11 outliers final: 6 residues processed: 136 average time/residue: 0.5588 time to fit residues: 81.6635 Evaluate side-chains 134 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain D residue 225 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 0.9990 chunk 97 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN E 171 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.149196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120138 restraints weight = 23674.212| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.92 r_work: 0.3186 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9098 Z= 0.125 Angle : 0.513 7.774 12313 Z= 0.270 Chirality : 0.042 0.157 1412 Planarity : 0.005 0.059 1537 Dihedral : 5.603 120.997 1252 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.44 % Allowed : 18.67 % Favored : 79.90 % 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 are not related in a simple way. whole: 1.20 (0.26), residues: 1118 helix: 2.26 (0.25), residues: 403 sheet: 0.48 (0.31), residues: 276 loop : -0.33 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 233 TYR 0.023 0.001 TYR E 235 PHE 0.025 0.001 PHE F 58 TRP 0.032 0.002 TRP F 117 HIS 0.003 0.001 HIS D 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 9094) covalent geometry : angle 0.51258 / 0.27 (12305) SS BOND : bond 0.00183 / 0.09 ( 4) SS BOND : angle 0.68896 / 0.34 ( 8) hydrogen bonds : bond 0.03198 / 2.10 ( 473) hydrogen bonds : angle 4.11606 / 2.91 ( 1327) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3570.33 seconds wall clock time: 61 minutes 46.47 seconds (3706.47 seconds total)