Starting phenix.real_space_refine on Wed Aug 5 04:31:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yh2_39279/08_2026/8yh2_39279.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yh2_39279/08_2026/8yh2_39279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yh2_39279/08_2026/8yh2_39279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yh2_39279/08_2026/8yh2_39279.map" model { file = "/net/cci-nas-00/data/ceres_data/8yh2_39279/08_2026/8yh2_39279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yh2_39279/08_2026/8yh2_39279.cif" } resolution = 3.27 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= 1.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5559 2.51 5 N 1462 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8690 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2198 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1700 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 208} Chain breaks: 2 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'ADN%rna3p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 2.07, per 1000 atoms: 0.24 Number of scatterers: 8690 At special positions: 0 Unit cell: (86.5037, 122.655, 123.946, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1603 8.00 N 1462 7.00 C 5559 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 114 " distance=2.04 Simple disulfide: pdb=" SG CYS B 114 " - pdb=" SG CYS B 121 " distance=2.07 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.05 Simple disulfide: pdb=" SG CYS R 83 " - pdb=" SG CYS R 165 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 0.73 Conformation dependent library (CDL) restraints added in 472.9 milliseconds 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 38.2% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.758A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 10 through 40 removed outlier: 3.503A pdb=" N ASN R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 44 Processing helix chain 'R' and resid 45 through 64 Processing helix chain 'R' and resid 64 through 75 removed outlier: 3.661A pdb=" N GLY R 75 " --> pdb=" O VAL R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 115 Processing helix chain 'R' and resid 117 through 122 Processing helix chain 'R' and resid 123 through 144 Processing helix chain 'R' and resid 145 through 148 Processing helix chain 'R' and resid 150 through 155 removed outlier: 4.246A pdb=" N SER R 154 " --> pdb=" O ASN R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.729A pdb=" N VAL R 170 " --> pdb=" O ARG R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 179 Processing helix chain 'R' and resid 179 through 185 Processing helix chain 'R' and resid 185 through 207 Processing helix chain 'R' and resid 225 through 254 Proline residue: R 244 - end of helix Processing helix chain 'R' and resid 259 through 282 removed outlier: 4.062A pdb=" N MET R 275 " --> pdb=" O HIS R 271 " (cutoff:3.500A) Proline residue: R 278 - end of helix removed outlier: 3.568A pdb=" N ALA R 282 " --> pdb=" O PRO R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 285 through 295 Processing helix chain 'A' and resid 8 through 31 removed outlier: 3.703A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.665A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.930A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.016A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 4.123A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.613A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.668A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 104 through 105 removed outlier: 4.514A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.591A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.768A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.419A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.531A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.408A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.576A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR S 50 " --> pdb=" O TYR S 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.342A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET S 218 " --> pdb=" O TYR S 163 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1185 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: 1.55 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 2790 1.36 - 1.50: 2392 1.50 - 1.63: 3593 1.63 - 1.77: 1 1.77 - 1.90: 97 Bond restraints: 8873 Sorted by residual: bond pdb=" C5 ADN R 801 " pdb=" N7 ADN R 801 " ideal model delta sigma weight residual 1.371 1.523 -0.152 2.00e-02 2.50e+03 5.80e+01 bond pdb=" C6 ADN R 801 " pdb=" N6 ADN R 801 " ideal model delta sigma weight residual 1.333 1.451 -0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" C8 ADN R 801 " pdb=" N9 ADN R 801 " ideal model delta sigma weight residual 1.370 1.255 0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C4 ADN R 801 " pdb=" C5 ADN R 801 " ideal model delta sigma weight residual 1.385 1.477 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C4 ADN R 801 " pdb=" N9 ADN R 801 " ideal model delta sigma weight residual 1.367 1.284 0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 8868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 11961 3.21 - 6.42: 45 6.42 - 9.62: 8 9.62 - 12.83: 2 12.83 - 16.04: 1 Bond angle restraints: 12017 Sorted by residual: angle pdb=" C4 ADN R 801 " pdb=" N9 ADN R 801 " pdb=" C8 ADN R 801 " ideal model delta sigma weight residual 105.99 122.03 -16.04 3.00e+00 1.11e-01 2.86e+01 angle pdb=" C CYS B 114 " pdb=" N GLY B 115 " pdb=" CA GLY B 115 " ideal model delta sigma weight residual 121.41 128.92 -7.51 1.96e+00 2.60e-01 1.47e+01 angle pdb=" CA PRO B 39 " pdb=" N PRO B 39 " pdb=" CD PRO B 39 " ideal model delta sigma weight residual 112.00 106.74 5.26 1.40e+00 5.10e-01 1.41e+01 angle pdb=" C6 ADN R 801 " pdb=" C5 ADN R 801 " pdb=" N7 ADN R 801 " ideal model delta sigma weight residual 132.88 143.60 -10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" C4 ADN R 801 " pdb=" C5 ADN R 801 " pdb=" N7 ADN R 801 " ideal model delta sigma weight residual 110.79 100.29 10.50 3.00e+00 1.11e-01 1.22e+01 ... (remaining 12012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 4686 16.11 - 32.22: 484 32.22 - 48.32: 83 48.32 - 64.43: 19 64.43 - 80.54: 8 Dihedral angle restraints: 5280 sinusoidal: 2078 harmonic: 3202 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 12.89 80.11 1 1.00e+01 1.00e-02 7.95e+01 dihedral pdb=" CA ALA B 113 " pdb=" C ALA B 113 " pdb=" N CYS B 114 " pdb=" CA CYS B 114 " ideal model delta harmonic sigma weight residual 180.00 138.11 41.89 0 5.00e+00 4.00e-02 7.02e+01 dihedral pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " pdb=" SG CYS B 114 " pdb=" CB CYS B 114 " ideal model delta sinusoidal sigma weight residual -86.00 -159.41 73.41 1 1.00e+01 1.00e-02 6.86e+01 ... (remaining 5277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1165 0.052 - 0.105: 155 0.105 - 0.157: 53 0.157 - 0.210: 1 0.210 - 0.262: 2 Chirality restraints: 1376 Sorted by residual: chirality pdb=" C3' ADN R 801 " pdb=" C2' ADN R 801 " pdb=" C4' ADN R 801 " pdb=" O3' ADN R 801 " both_signs ideal model delta sigma weight residual False -2.48 -2.74 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C2' ADN R 801 " pdb=" C1' ADN R 801 " pdb=" C3' ADN R 801 " pdb=" O2' ADN R 801 " both_signs ideal model delta sigma weight residual False -2.75 -2.50 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA CYS B 114 " pdb=" N CYS B 114 " pdb=" C CYS B 114 " pdb=" CB CYS B 114 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.14e-01 ... (remaining 1373 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " -0.051 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO B 39 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.047 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO S 75 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 113 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C ALA B 113 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA B 113 " 0.012 2.00e-02 2.50e+03 pdb=" N CYS B 114 " 0.010 2.00e-02 2.50e+03 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 91 2.57 - 3.16: 7447 3.16 - 3.74: 13233 3.74 - 4.32: 18735 4.32 - 4.90: 31575 Nonbonded interactions: 71081 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 1.993 3.040 nonbonded pdb=" OE1 GLN S 130 " pdb=" OG1 THR S 231 " model vdw 2.017 3.040 nonbonded pdb=" OE2 GLU R 19 " pdb=" ND1 HIS R 271 " model vdw 2.074 3.120 nonbonded pdb=" OG SER B 281 " pdb=" O HIS G 44 " model vdw 2.096 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.105 3.040 ... (remaining 71076 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.760 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 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 0.152 8879 Z= 0.200 Angle : 0.640 16.040 12029 Z= 0.343 Chirality : 0.042 0.262 1376 Planarity : 0.004 0.075 1498 Dihedral : 13.420 80.539 3196 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.26), residues: 1085 helix: 1.71 (0.28), residues: 365 sheet: -0.69 (0.32), residues: 263 loop : -0.95 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.017 0.001 TYR S 178 PHE 0.011 0.001 PHE B 234 TRP 0.015 0.001 TRP R 35 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.20 ( 8873) covalent geometry : angle 0.62856 / 0.34 (12017) SS BOND : bond 0.01835 / 0.88 ( 6) SS BOND : angle 3.84553 / 1.90 ( 12) hydrogen bonds : bond 0.19777 / 13.18 ( 424) hydrogen bonds : angle 7.17764 / 5.24 ( 1185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ASN cc_start: 0.5302 (p0) cc_final: 0.4840 (p0) REVERT: A 337 ASP cc_start: 0.7298 (m-30) cc_final: 0.6593 (m-30) REVERT: S 38 ARG cc_start: 0.6515 (ptt180) cc_final: 0.5803 (ptt180) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1182 time to fit residues: 42.4511 Evaluate side-chains 183 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN S 39 GLN S 82 GLN S 171 GLN ** S 219 GLN ** 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 = 0.4149 r_free = 0.4149 target = 0.126700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.104828 restraints weight = 22612.400| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 4.48 r_work: 0.3642 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 8879 Z= 0.193 Angle : 0.775 12.701 12029 Z= 0.405 Chirality : 0.048 0.228 1376 Planarity : 0.005 0.056 1498 Dihedral : 5.816 59.308 1214 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 2.10 % Allowed : 12.07 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.26), residues: 1085 helix: 1.52 (0.27), residues: 375 sheet: -0.60 (0.30), residues: 268 loop : -0.98 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 168 TYR 0.014 0.002 TYR A 287 PHE 0.020 0.002 PHE R 167 TRP 0.027 0.002 TRP R 184 HIS 0.004 0.001 HIS R 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 ( 8873) covalent geometry : angle 0.75179 / 0.39 (12017) SS BOND : bond 0.02125 / 1.02 ( 6) SS BOND : angle 5.94767 / 3.09 ( 12) hydrogen bonds : bond 0.05451 / 3.78 ( 424) hydrogen bonds : angle 5.71178 / 4.19 ( 1185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 325 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8622 (mmm) REVERT: G 15 LEU cc_start: 0.9161 (tt) cc_final: 0.8949 (pp) REVERT: G 42 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7583 (pt0) REVERT: G 44 HIS cc_start: 0.8136 (m-70) cc_final: 0.7269 (t70) REVERT: G 47 GLU cc_start: 0.8210 (tp30) cc_final: 0.7991 (tm-30) REVERT: R 119 ARG cc_start: 0.6967 (tpp-160) cc_final: 0.6761 (tpp-160) REVERT: R 128 TRP cc_start: 0.7506 (m100) cc_final: 0.7181 (m100) REVERT: A 18 MET cc_start: 0.8240 (tpp) cc_final: 0.7626 (mmm) REVERT: A 22 ASN cc_start: 0.7225 (m110) cc_final: 0.6693 (m-40) REVERT: A 256 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.8225 (p0) REVERT: A 269 ASN cc_start: 0.6352 (p0) cc_final: 0.5929 (p0) REVERT: A 308 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8885 (mm-30) REVERT: A 333 GLN cc_start: 0.8009 (tp-100) cc_final: 0.7698 (tp-100) REVERT: A 337 ASP cc_start: 0.7580 (m-30) cc_final: 0.7085 (m-30) REVERT: S 82 GLN cc_start: 0.7705 (tp40) cc_final: 0.7379 (tp-100) REVERT: S 93 MET cc_start: 0.9041 (ttm) cc_final: 0.8755 (tmm) REVERT: S 128 MET cc_start: 0.5210 (OUTLIER) cc_final: 0.4851 (mtp) REVERT: S 148 ARG cc_start: 0.7892 (mmm-85) cc_final: 0.7265 (mmm-85) REVERT: S 208 GLU cc_start: 0.8362 (mp0) cc_final: 0.8093 (mp0) outliers start: 20 outliers final: 11 residues processed: 216 average time/residue: 0.1088 time to fit residues: 31.7233 Evaluate side-chains 184 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.117109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.095411 restraints weight = 23699.256| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 4.40 r_work: 0.3486 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.113 8879 Z= 0.350 Angle : 0.903 17.777 12029 Z= 0.472 Chirality : 0.052 0.215 1376 Planarity : 0.005 0.060 1498 Dihedral : 6.345 58.330 1214 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.21 % Rotamer: Outliers : 3.88 % Allowed : 16.89 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.25), residues: 1085 helix: 0.67 (0.26), residues: 379 sheet: -0.74 (0.30), residues: 266 loop : -1.21 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 126 TYR 0.028 0.003 TYR S 178 PHE 0.018 0.002 PHE R 200 TRP 0.021 0.003 TRP B 82 HIS 0.009 0.002 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00798 / 0.35 ( 8873) covalent geometry : angle 0.87827 / 0.46 (12017) SS BOND : bond 0.02395 / 1.18 ( 6) SS BOND : angle 6.73924 / 3.65 ( 12) hydrogen bonds : bond 0.06370 / 4.47 ( 424) hydrogen bonds : angle 5.82778 / 4.31 ( 1185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 ILE cc_start: 0.7512 (mp) cc_final: 0.7289 (mp) REVERT: B 262 MET cc_start: 0.7767 (mmm) cc_final: 0.7478 (mmm) REVERT: B 264 TYR cc_start: 0.7867 (m-80) cc_final: 0.7584 (m-10) REVERT: B 325 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8322 (ptp) REVERT: B 337 LYS cc_start: 0.7963 (mttm) cc_final: 0.7720 (mttp) REVERT: G 21 MET cc_start: 0.9329 (mmp) cc_final: 0.9106 (mmm) REVERT: G 42 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7919 (pp20) REVERT: G 44 HIS cc_start: 0.8320 (m-70) cc_final: 0.7444 (t70) REVERT: G 46 LYS cc_start: 0.9427 (tppt) cc_final: 0.9150 (tppt) REVERT: R 173 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7289 (mmt) REVERT: A 194 LEU cc_start: 0.9314 (mt) cc_final: 0.9076 (tt) REVERT: A 256 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8382 (p0) REVERT: A 269 ASN cc_start: 0.6211 (p0) cc_final: 0.5573 (p0) REVERT: A 287 TYR cc_start: 0.6196 (t80) cc_final: 0.5887 (t80) REVERT: A 333 GLN cc_start: 0.8341 (tp-100) cc_final: 0.7877 (tp-100) REVERT: A 337 ASP cc_start: 0.7683 (m-30) cc_final: 0.7016 (m-30) REVERT: S 34 MET cc_start: 0.5880 (mmp) cc_final: 0.5354 (mmm) REVERT: S 50 TYR cc_start: 0.8477 (t80) cc_final: 0.8111 (t80) REVERT: S 82 GLN cc_start: 0.7569 (tp40) cc_final: 0.7126 (tp-100) REVERT: S 109 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7725 (m-30) outliers start: 37 outliers final: 27 residues processed: 194 average time/residue: 0.1101 time to fit residues: 28.8010 Evaluate side-chains 188 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 275 MET Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 12 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 ASN G 44 HIS A 22 ASN S 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.121656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.099436 restraints weight = 23572.838| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 4.56 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8879 Z= 0.154 Angle : 0.731 13.301 12029 Z= 0.380 Chirality : 0.046 0.228 1376 Planarity : 0.005 0.060 1498 Dihedral : 5.858 56.597 1214 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % Rotamer: Outliers : 3.36 % Allowed : 18.68 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.26), residues: 1085 helix: 1.39 (0.27), residues: 378 sheet: -0.61 (0.30), residues: 261 loop : -1.14 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 27 TYR 0.028 0.002 TYR S 178 PHE 0.018 0.002 PHE S 32 TRP 0.029 0.002 TRP R 184 HIS 0.007 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 8873) covalent geometry : angle 0.71384 / 0.37 (12017) SS BOND : bond 0.01877 / 0.90 ( 6) SS BOND : angle 5.09766 / 2.76 ( 12) hydrogen bonds : bond 0.04957 / 3.48 ( 424) hydrogen bonds : angle 5.31690 / 3.95 ( 1185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8407 (mm110) cc_final: 0.8070 (mp10) REVERT: B 215 GLU cc_start: 0.9044 (mp0) cc_final: 0.8659 (mp0) REVERT: B 217 MET cc_start: 0.8737 (ptt) cc_final: 0.7812 (pmm) REVERT: B 262 MET cc_start: 0.7383 (mmm) cc_final: 0.6936 (mmm) REVERT: B 264 TYR cc_start: 0.7626 (m-80) cc_final: 0.7369 (m-10) REVERT: B 325 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8028 (ttp) REVERT: G 42 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7692 (pt0) REVERT: G 44 HIS cc_start: 0.8074 (m170) cc_final: 0.7448 (t70) REVERT: G 46 LYS cc_start: 0.9380 (tppt) cc_final: 0.9164 (tppt) REVERT: G 47 GLU cc_start: 0.8438 (tp30) cc_final: 0.7812 (tm-30) REVERT: A 22 ASN cc_start: 0.7174 (m110) cc_final: 0.6925 (m110) REVERT: A 212 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8775 (tp) REVERT: A 250 PHE cc_start: 0.8698 (t80) cc_final: 0.8412 (t80) REVERT: A 269 ASN cc_start: 0.6374 (p0) cc_final: 0.5993 (p0) REVERT: A 302 TYR cc_start: 0.8376 (t80) cc_final: 0.7599 (t80) REVERT: A 314 LYS cc_start: 0.9026 (mppt) cc_final: 0.8681 (mttm) REVERT: A 333 GLN cc_start: 0.8328 (tp-100) cc_final: 0.7991 (tp-100) REVERT: A 351 CYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6956 (m) REVERT: S 34 MET cc_start: 0.5382 (mmp) cc_final: 0.4969 (mmm) REVERT: S 82 GLN cc_start: 0.7374 (tp40) cc_final: 0.6932 (tp-100) REVERT: S 206 ARG cc_start: 0.8746 (mmp80) cc_final: 0.8516 (mmp80) REVERT: S 208 GLU cc_start: 0.7732 (mp0) cc_final: 0.7501 (mp0) outliers start: 32 outliers final: 21 residues processed: 191 average time/residue: 0.1142 time to fit residues: 29.1357 Evaluate side-chains 185 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 3 optimal weight: 0.0050 chunk 19 optimal weight: 0.5980 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.122840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.100774 restraints weight = 23100.432| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 4.45 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8879 Z= 0.145 Angle : 0.698 12.806 12029 Z= 0.362 Chirality : 0.044 0.231 1376 Planarity : 0.004 0.059 1498 Dihedral : 5.707 58.367 1214 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 3.57 % Allowed : 19.52 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.26), residues: 1085 helix: 1.65 (0.27), residues: 376 sheet: -0.56 (0.30), residues: 267 loop : -1.18 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 206 TYR 0.026 0.002 TYR S 178 PHE 0.014 0.001 PHE R 288 TRP 0.029 0.002 TRP B 211 HIS 0.008 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 8873) covalent geometry : angle 0.68130 / 0.35 (12017) SS BOND : bond 0.01753 / 0.85 ( 6) SS BOND : angle 4.80696 / 2.60 ( 12) hydrogen bonds : bond 0.04635 / 3.27 ( 424) hydrogen bonds : angle 5.10137 / 3.81 ( 1185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6925 (mp) REVERT: B 175 GLN cc_start: 0.8451 (mm110) cc_final: 0.8072 (mp10) REVERT: B 215 GLU cc_start: 0.8905 (mp0) cc_final: 0.8647 (pm20) REVERT: B 217 MET cc_start: 0.8597 (ptt) cc_final: 0.8277 (ptt) REVERT: B 262 MET cc_start: 0.7294 (mmm) cc_final: 0.6829 (mmm) REVERT: B 264 TYR cc_start: 0.7521 (m-80) cc_final: 0.7274 (m-10) REVERT: B 325 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8060 (mmm) REVERT: B 337 LYS cc_start: 0.7508 (mttm) cc_final: 0.7257 (mttp) REVERT: G 42 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7790 (pt0) REVERT: G 44 HIS cc_start: 0.8130 (m170) cc_final: 0.7591 (t70) REVERT: G 47 GLU cc_start: 0.8223 (tp30) cc_final: 0.7694 (tm-30) REVERT: R 68 LEU cc_start: 0.7609 (mt) cc_final: 0.7192 (tp) REVERT: R 176 MET cc_start: 0.5782 (OUTLIER) cc_final: 0.5501 (tmm) REVERT: A 25 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8028 (pt0) REVERT: A 216 GLU cc_start: 0.8536 (tp30) cc_final: 0.8301 (tp30) REVERT: A 269 ASN cc_start: 0.6441 (p0) cc_final: 0.5925 (p0) REVERT: A 314 LYS cc_start: 0.9031 (mppt) cc_final: 0.8755 (mttm) REVERT: A 333 GLN cc_start: 0.8379 (tp-100) cc_final: 0.8030 (tp-100) REVERT: A 341 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8197 (t0) REVERT: A 351 CYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6838 (m) REVERT: S 34 MET cc_start: 0.5459 (mmp) cc_final: 0.4995 (mmm) REVERT: S 38 ARG cc_start: 0.7378 (ptt180) cc_final: 0.6972 (ptt180) REVERT: S 82 GLN cc_start: 0.7500 (tp40) cc_final: 0.7034 (tp40) REVERT: S 93 MET cc_start: 0.8594 (ttp) cc_final: 0.8113 (tmm) REVERT: S 206 ARG cc_start: 0.8734 (mmp80) cc_final: 0.8439 (mmp80) REVERT: S 208 GLU cc_start: 0.7926 (mp0) cc_final: 0.7409 (mp0) outliers start: 34 outliers final: 20 residues processed: 192 average time/residue: 0.1091 time to fit residues: 28.1250 Evaluate side-chains 186 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 176 MET Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.122610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.100607 restraints weight = 23092.269| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 4.46 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8879 Z= 0.155 Angle : 0.704 12.960 12029 Z= 0.365 Chirality : 0.045 0.235 1376 Planarity : 0.004 0.057 1498 Dihedral : 5.674 58.232 1214 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 3.36 % Allowed : 20.78 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.26), residues: 1085 helix: 1.67 (0.27), residues: 376 sheet: -0.43 (0.31), residues: 259 loop : -1.23 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 148 TYR 0.024 0.002 TYR S 178 PHE 0.024 0.001 PHE A 250 TRP 0.021 0.002 TRP B 211 HIS 0.007 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 8873) covalent geometry : angle 0.68731 / 0.36 (12017) SS BOND : bond 0.01667 / 0.81 ( 6) SS BOND : angle 4.86374 / 2.63 ( 12) hydrogen bonds : bond 0.04642 / 3.26 ( 424) hydrogen bonds : angle 5.06078 / 3.78 ( 1185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7826 (mmt180) cc_final: 0.7398 (mmm160) REVERT: B 37 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6865 (mp) REVERT: B 175 GLN cc_start: 0.8471 (mm110) cc_final: 0.8108 (mp10) REVERT: B 215 GLU cc_start: 0.8923 (mp0) cc_final: 0.8666 (pm20) REVERT: B 217 MET cc_start: 0.8627 (ptt) cc_final: 0.8277 (ptt) REVERT: B 262 MET cc_start: 0.7539 (mmm) cc_final: 0.7001 (mmm) REVERT: B 325 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8058 (mmm) REVERT: B 337 LYS cc_start: 0.7533 (mttm) cc_final: 0.7287 (mttp) REVERT: G 42 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7835 (pt0) REVERT: G 44 HIS cc_start: 0.8022 (m170) cc_final: 0.7624 (t70) REVERT: R 68 LEU cc_start: 0.7639 (mt) cc_final: 0.7201 (tp) REVERT: R 275 MET cc_start: 0.6837 (OUTLIER) cc_final: 0.6528 (tmm) REVERT: A 25 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8125 (pt0) REVERT: A 214 CYS cc_start: 0.8755 (m) cc_final: 0.8455 (t) REVERT: A 269 ASN cc_start: 0.6385 (p0) cc_final: 0.5669 (p0) REVERT: A 302 TYR cc_start: 0.8225 (t80) cc_final: 0.7421 (t80) REVERT: A 314 LYS cc_start: 0.9020 (mppt) cc_final: 0.8744 (mttm) REVERT: A 333 GLN cc_start: 0.8359 (tp-100) cc_final: 0.8008 (tp-100) REVERT: A 351 CYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6995 (m) REVERT: S 34 MET cc_start: 0.5492 (mmp) cc_final: 0.5047 (mmm) REVERT: S 82 GLN cc_start: 0.7468 (tp40) cc_final: 0.6994 (tp40) REVERT: S 93 MET cc_start: 0.8544 (ttp) cc_final: 0.8174 (tmm) REVERT: S 206 ARG cc_start: 0.8779 (mmp80) cc_final: 0.8564 (mmp80) REVERT: S 208 GLU cc_start: 0.8313 (mp0) cc_final: 0.7811 (mp0) REVERT: S 210 GLU cc_start: 0.7442 (pm20) cc_final: 0.7058 (pm20) outliers start: 32 outliers final: 22 residues processed: 182 average time/residue: 0.0906 time to fit residues: 22.2664 Evaluate side-chains 181 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 275 MET Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 76 optimal weight: 0.0170 chunk 29 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 295 ASN R 95 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.119329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.097596 restraints weight = 23261.664| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 4.32 r_work: 0.3598 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8879 Z= 0.174 Angle : 0.756 15.982 12029 Z= 0.386 Chirality : 0.045 0.239 1376 Planarity : 0.004 0.053 1498 Dihedral : 5.600 55.962 1214 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.39 % Rotamer: Outliers : 3.57 % Allowed : 21.62 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.26), residues: 1085 helix: 1.71 (0.27), residues: 378 sheet: -0.49 (0.30), residues: 265 loop : -1.25 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 148 TYR 0.018 0.002 TYR A 302 PHE 0.016 0.002 PHE A 250 TRP 0.018 0.002 TRP B 211 HIS 0.007 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 8873) covalent geometry : angle 0.73974 / 0.38 (12017) SS BOND : bond 0.01821 / 0.87 ( 6) SS BOND : angle 4.96430 / 2.68 ( 12) hydrogen bonds : bond 0.04728 / 3.33 ( 424) hydrogen bonds : angle 5.09817 / 3.83 ( 1185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7722 (mmt180) cc_final: 0.6972 (mmm160) REVERT: B 37 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.7030 (mp) REVERT: B 75 GLN cc_start: 0.8558 (tt0) cc_final: 0.8268 (mt0) REVERT: B 175 GLN cc_start: 0.8730 (mm110) cc_final: 0.8350 (mp10) REVERT: B 217 MET cc_start: 0.8716 (ptt) cc_final: 0.8306 (ptt) REVERT: B 262 MET cc_start: 0.7792 (mmm) cc_final: 0.7254 (mmm) REVERT: B 264 TYR cc_start: 0.7586 (m-80) cc_final: 0.7346 (m-10) REVERT: B 325 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8219 (ttp) REVERT: B 337 LYS cc_start: 0.7826 (mttm) cc_final: 0.7598 (mttp) REVERT: G 42 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7859 (pt0) REVERT: G 44 HIS cc_start: 0.8093 (m170) cc_final: 0.7547 (t-170) REVERT: R 68 LEU cc_start: 0.7802 (mt) cc_final: 0.7352 (tp) REVERT: A 25 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8150 (pt0) REVERT: A 214 CYS cc_start: 0.9212 (m) cc_final: 0.8807 (t) REVERT: A 269 ASN cc_start: 0.6299 (p0) cc_final: 0.5635 (p0) REVERT: A 302 TYR cc_start: 0.8282 (t80) cc_final: 0.8067 (t80) REVERT: A 314 LYS cc_start: 0.9054 (mppt) cc_final: 0.8780 (mttp) REVERT: A 333 GLN cc_start: 0.8450 (tp-100) cc_final: 0.8102 (tp-100) REVERT: A 351 CYS cc_start: 0.7473 (OUTLIER) cc_final: 0.6911 (m) REVERT: S 34 MET cc_start: 0.5709 (mmp) cc_final: 0.5284 (mmm) REVERT: S 82 GLN cc_start: 0.7711 (tp40) cc_final: 0.7241 (tp40) REVERT: S 206 ARG cc_start: 0.8918 (mmp80) cc_final: 0.8671 (mmp80) REVERT: S 208 GLU cc_start: 0.8410 (mp0) cc_final: 0.7929 (mp0) REVERT: S 210 GLU cc_start: 0.7391 (pm20) cc_final: 0.7116 (pm20) outliers start: 34 outliers final: 27 residues processed: 180 average time/residue: 0.0864 time to fit residues: 20.9711 Evaluate side-chains 183 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 42 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.122709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.101327 restraints weight = 22912.818| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 4.40 r_work: 0.3617 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8879 Z= 0.161 Angle : 0.756 12.342 12029 Z= 0.389 Chirality : 0.045 0.247 1376 Planarity : 0.004 0.052 1498 Dihedral : 5.508 52.757 1214 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 3.99 % Allowed : 21.62 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.26), residues: 1085 helix: 1.74 (0.27), residues: 378 sheet: -0.54 (0.30), residues: 265 loop : -1.23 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 27 TYR 0.026 0.002 TYR S 178 PHE 0.012 0.002 PHE S 200 TRP 0.051 0.002 TRP B 211 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 8873) covalent geometry : angle 0.74236 / 0.38 (12017) SS BOND : bond 0.01726 / 0.83 ( 6) SS BOND : angle 4.62654 / 2.50 ( 12) hydrogen bonds : bond 0.04630 / 3.27 ( 424) hydrogen bonds : angle 5.07509 / 3.83 ( 1185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7721 (mmt180) cc_final: 0.6953 (mmm160) REVERT: B 37 ILE cc_start: 0.7293 (OUTLIER) cc_final: 0.7020 (mp) REVERT: B 101 MET cc_start: 0.6572 (mpp) cc_final: 0.5770 (mmm) REVERT: B 130 GLU cc_start: 0.8363 (tt0) cc_final: 0.7985 (tt0) REVERT: B 175 GLN cc_start: 0.8724 (mm110) cc_final: 0.8344 (mp10) REVERT: B 264 TYR cc_start: 0.7611 (m-80) cc_final: 0.7311 (m-10) REVERT: B 325 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8347 (mmm) REVERT: B 337 LYS cc_start: 0.7752 (mttm) cc_final: 0.7528 (mttp) REVERT: G 42 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7706 (pt0) REVERT: G 44 HIS cc_start: 0.8316 (m170) cc_final: 0.7928 (t-170) REVERT: G 47 GLU cc_start: 0.8032 (tp30) cc_final: 0.7786 (tp30) REVERT: R 68 LEU cc_start: 0.7739 (mt) cc_final: 0.7344 (tp) REVERT: A 25 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8132 (pt0) REVERT: A 214 CYS cc_start: 0.9206 (m) cc_final: 0.8919 (t) REVERT: A 269 ASN cc_start: 0.7035 (p0) cc_final: 0.6325 (p0) REVERT: A 302 TYR cc_start: 0.8312 (t80) cc_final: 0.7960 (t80) REVERT: A 303 ILE cc_start: 0.9259 (mt) cc_final: 0.9056 (mm) REVERT: A 304 GLN cc_start: 0.8786 (tt0) cc_final: 0.8559 (tt0) REVERT: A 314 LYS cc_start: 0.9061 (mppt) cc_final: 0.8764 (mttm) REVERT: A 333 GLN cc_start: 0.8416 (tp-100) cc_final: 0.8104 (tp-100) REVERT: A 351 CYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7065 (m) REVERT: S 34 MET cc_start: 0.5683 (mmp) cc_final: 0.5330 (mmm) REVERT: S 82 GLN cc_start: 0.7711 (tp40) cc_final: 0.7227 (tp-100) REVERT: S 93 MET cc_start: 0.8901 (ptm) cc_final: 0.8632 (tmm) REVERT: S 206 ARG cc_start: 0.8913 (mmp80) cc_final: 0.8667 (mmp80) REVERT: S 208 GLU cc_start: 0.8386 (mp0) cc_final: 0.7914 (mp0) REVERT: S 210 GLU cc_start: 0.7426 (pm20) cc_final: 0.7171 (pm20) outliers start: 38 outliers final: 27 residues processed: 185 average time/residue: 0.0771 time to fit residues: 19.5269 Evaluate side-chains 189 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 30 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.124751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.102941 restraints weight = 22995.241| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 4.45 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8879 Z= 0.145 Angle : 0.761 10.318 12029 Z= 0.391 Chirality : 0.045 0.255 1376 Planarity : 0.004 0.055 1498 Dihedral : 5.444 51.747 1214 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 3.67 % Allowed : 21.93 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.26), residues: 1085 helix: 1.86 (0.27), residues: 377 sheet: -0.68 (0.30), residues: 272 loop : -1.17 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 27 TYR 0.028 0.002 TYR S 178 PHE 0.024 0.001 PHE A 250 TRP 0.063 0.002 TRP B 211 HIS 0.012 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8873) covalent geometry : angle 0.75126 / 0.39 (12017) SS BOND : bond 0.01409 / 0.67 ( 6) SS BOND : angle 3.86540 / 2.09 ( 12) hydrogen bonds : bond 0.04440 / 3.12 ( 424) hydrogen bonds : angle 5.08364 / 3.82 ( 1185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.8086 (mmt180) cc_final: 0.7621 (mmm160) REVERT: B 37 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6848 (mp) REVERT: B 75 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8249 (mt0) REVERT: B 78 LYS cc_start: 0.8357 (tppt) cc_final: 0.8129 (mttm) REVERT: B 101 MET cc_start: 0.6210 (mpp) cc_final: 0.5139 (mmm) REVERT: B 138 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7633 (mm-30) REVERT: B 175 GLN cc_start: 0.8456 (mm110) cc_final: 0.8200 (mp10) REVERT: B 262 MET cc_start: 0.7833 (mmm) cc_final: 0.7567 (mmm) REVERT: B 337 LYS cc_start: 0.7532 (mttm) cc_final: 0.7275 (mttp) REVERT: G 42 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7798 (pt0) REVERT: G 44 HIS cc_start: 0.8181 (m170) cc_final: 0.7917 (t-170) REVERT: R 68 LEU cc_start: 0.7469 (mt) cc_final: 0.7112 (tp) REVERT: R 133 LEU cc_start: 0.7534 (tt) cc_final: 0.7264 (mm) REVERT: A 25 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8094 (pt0) REVERT: A 29 LYS cc_start: 0.8318 (tppt) cc_final: 0.7982 (tppt) REVERT: A 214 CYS cc_start: 0.8881 (m) cc_final: 0.8565 (t) REVERT: A 269 ASN cc_start: 0.6794 (p0) cc_final: 0.6089 (p0) REVERT: A 314 LYS cc_start: 0.9043 (mppt) cc_final: 0.8757 (mttp) REVERT: A 333 GLN cc_start: 0.8351 (tp-100) cc_final: 0.8033 (tp-100) REVERT: A 351 CYS cc_start: 0.7370 (OUTLIER) cc_final: 0.6997 (m) REVERT: S 34 MET cc_start: 0.5580 (mmp) cc_final: 0.5215 (mmm) REVERT: S 82 GLN cc_start: 0.7533 (tp40) cc_final: 0.7274 (mm-40) REVERT: S 206 ARG cc_start: 0.8767 (mmp80) cc_final: 0.8510 (mmp80) REVERT: S 208 GLU cc_start: 0.8276 (mp0) cc_final: 0.7843 (mp0) outliers start: 35 outliers final: 27 residues processed: 187 average time/residue: 0.0871 time to fit residues: 22.1958 Evaluate side-chains 187 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 72 optimal weight: 0.0060 chunk 2 optimal weight: 30.0000 chunk 103 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.128699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.106859 restraints weight = 22660.418| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 4.50 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8879 Z= 0.143 Angle : 0.769 10.485 12029 Z= 0.395 Chirality : 0.045 0.261 1376 Planarity : 0.004 0.058 1498 Dihedral : 5.360 48.466 1214 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.94 % Rotamer: Outliers : 3.46 % Allowed : 22.14 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.26), residues: 1085 helix: 1.84 (0.27), residues: 378 sheet: -0.71 (0.30), residues: 272 loop : -1.17 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 27 TYR 0.028 0.002 TYR S 178 PHE 0.015 0.001 PHE A 250 TRP 0.060 0.002 TRP B 211 HIS 0.008 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 8873) covalent geometry : angle 0.76132 / 0.39 (12017) SS BOND : bond 0.01161 / 0.55 ( 6) SS BOND : angle 3.45317 / 1.88 ( 12) hydrogen bonds : bond 0.04371 / 3.06 ( 424) hydrogen bonds : angle 5.08297 / 3.78 ( 1185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.8130 (mmt180) cc_final: 0.7711 (mmm160) REVERT: B 37 ILE cc_start: 0.7191 (OUTLIER) cc_final: 0.6973 (mp) REVERT: B 75 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8092 (mt0) REVERT: B 101 MET cc_start: 0.6062 (mpp) cc_final: 0.5514 (mmm) REVERT: B 138 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7569 (mm-30) REVERT: B 175 GLN cc_start: 0.8375 (mm110) cc_final: 0.8151 (mp10) REVERT: B 262 MET cc_start: 0.7859 (mmm) cc_final: 0.7609 (mmm) REVERT: B 264 TYR cc_start: 0.7216 (m-10) cc_final: 0.7003 (m-10) REVERT: B 337 LYS cc_start: 0.7457 (mttm) cc_final: 0.7194 (mttp) REVERT: G 44 HIS cc_start: 0.8181 (m170) cc_final: 0.7904 (t70) REVERT: R 68 LEU cc_start: 0.7440 (mt) cc_final: 0.7064 (tp) REVERT: A 18 MET cc_start: 0.7418 (mmm) cc_final: 0.7134 (tpp) REVERT: A 25 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8078 (pt0) REVERT: A 29 LYS cc_start: 0.8299 (tppt) cc_final: 0.7919 (tppt) REVERT: A 214 CYS cc_start: 0.8799 (m) cc_final: 0.8570 (t) REVERT: A 314 LYS cc_start: 0.9069 (mppt) cc_final: 0.8748 (mttp) REVERT: A 333 GLN cc_start: 0.8293 (tp-100) cc_final: 0.8021 (tp40) REVERT: A 351 CYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6600 (m) REVERT: S 34 MET cc_start: 0.5607 (mmp) cc_final: 0.5221 (mmm) REVERT: S 82 GLN cc_start: 0.7484 (tp40) cc_final: 0.7050 (tp40) REVERT: S 93 MET cc_start: 0.8242 (tmm) cc_final: 0.7938 (ppp) REVERT: S 171 GLN cc_start: 0.8398 (mp10) cc_final: 0.8140 (mp10) REVERT: S 208 GLU cc_start: 0.8201 (mp0) cc_final: 0.7824 (mp0) outliers start: 33 outliers final: 26 residues processed: 184 average time/residue: 0.0841 time to fit residues: 21.1051 Evaluate side-chains 186 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 29 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.121425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.099494 restraints weight = 22908.703| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 4.39 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8879 Z= 0.176 Angle : 0.796 12.281 12029 Z= 0.416 Chirality : 0.045 0.195 1376 Planarity : 0.005 0.059 1498 Dihedral : 5.358 46.923 1214 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.61 % Favored : 95.30 % Rotamer: Outliers : 3.15 % Allowed : 22.67 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.26), residues: 1085 helix: 1.57 (0.27), residues: 383 sheet: -0.67 (0.30), residues: 266 loop : -1.25 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 148 TYR 0.059 0.002 TYR A 302 PHE 0.020 0.002 PHE A 250 TRP 0.059 0.002 TRP B 211 HIS 0.010 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 8873) covalent geometry : angle 0.78752 / 0.41 (12017) SS BOND : bond 0.01327 / 0.63 ( 6) SS BOND : angle 3.80719 / 2.09 ( 12) hydrogen bonds : bond 0.04694 / 3.31 ( 424) hydrogen bonds : angle 5.11589 / 3.78 ( 1185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2146.36 seconds wall clock time: 37 minutes 42.82 seconds (2262.82 seconds total)