Starting phenix.real_space_refine on Wed Sep 17 12:10:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yh2_39279/09_2025/8yh2_39279.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yh2_39279/09_2025/8yh2_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yh2_39279/09_2025/8yh2_39279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yh2_39279/09_2025/8yh2_39279.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yh2_39279/09_2025/8yh2_39279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yh2_39279/09_2025/8yh2_39279.map" } 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-2.0-5805/lib/python3.9/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: 2.62, per 1000 atoms: 0.30 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: 1.14 Conformation dependent library (CDL) restraints added in 409.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.32 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: 1.43 Time building geometry restraints manager: 1.44 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: 11962 3.21 - 6.42: 44 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 - 0.050: 1138 0.050 - 0.100: 173 0.100 - 0.150: 60 0.150 - 0.200: 4 0.200 - 0.249: 1 Chirality restraints: 1376 Sorted by residual: 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 1.55e+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 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 -2.56 -2.74 0.18 2.00e-01 2.50e+01 7.90e-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: 0.380 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.340 Find NCS groups from input model: 0.040 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 13.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 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= 0.201 Angle : 0.640 16.040 12029 Z= 0.340 Chirality : 0.042 0.249 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 aren 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 covalent geometry : bond 0.00423 ( 8873) covalent geometry : angle 0.62865 (12017) SS BOND : bond 0.01835 ( 6) SS BOND : angle 3.84553 ( 12) hydrogen bonds : bond 0.19777 ( 424) hydrogen bonds : angle 7.17764 ( 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 : 0.431 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: 0.5301 (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: 0.1198 time to fit residues: 42.6846 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 : 0.348 ------------------------------------------------------------------------------- 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: 6.9990 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4150 r_free = 0.4150 target = 0.126751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.104821 restraints weight = 22618.402| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 4.49 r_work: 0.3643 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 8879 Z= 0.195 Angle : 0.774 12.532 12029 Z= 0.405 Chirality : 0.048 0.228 1376 Planarity : 0.005 0.059 1498 Dihedral : 5.803 58.880 1214 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 2.20 % Allowed : 12.17 % Favored : 85.62 % 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 aren not related in a simple way. whole: -0.08 (0.26), residues: 1085 helix: 1.48 (0.27), residues: 375 sheet: -0.61 (0.30), residues: 268 loop : -0.97 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 137 TYR 0.014 0.002 TYR A 287 PHE 0.021 0.002 PHE R 167 TRP 0.025 0.002 TRP R 184 HIS 0.004 0.001 HIS R 95 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 8873) covalent geometry : angle 0.75259 (12017) SS BOND : bond 0.02237 ( 6) SS BOND : angle 5.81752 ( 12) hydrogen bonds : bond 0.05374 ( 424) hydrogen bonds : angle 5.68940 ( 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: 21 poor density : 207 time to evaluate : 0.294 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: B 215 GLU cc_start: 0.9308 (mp0) cc_final: 0.8956 (mp0) REVERT: B 325 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8615 (mmm) REVERT: G 15 LEU cc_start: 0.9164 (tt) cc_final: 0.8954 (pp) REVERT: G 42 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7588 (pt0) REVERT: G 44 HIS cc_start: 0.8131 (m-70) cc_final: 0.7282 (t70) REVERT: R 128 TRP cc_start: 0.7680 (m100) cc_final: 0.7307 (m100) REVERT: A 18 MET cc_start: 0.8250 (tpp) cc_final: 0.7446 (tpp) REVERT: A 22 ASN cc_start: 0.7228 (m110) cc_final: 0.6618 (m-40) REVERT: A 256 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8207 (p0) REVERT: A 269 ASN cc_start: 0.6508 (p0) cc_final: 0.6162 (p0) REVERT: A 333 GLN cc_start: 0.8067 (tp-100) cc_final: 0.7796 (tp-100) REVERT: A 337 ASP cc_start: 0.7579 (m-30) cc_final: 0.7097 (m-30) REVERT: A 349 LYS cc_start: 0.8087 (ttpt) cc_final: 0.7882 (ttpp) REVERT: S 82 GLN cc_start: 0.7719 (tp40) cc_final: 0.7393 (tp-100) REVERT: S 208 GLU cc_start: 0.8361 (mp0) cc_final: 0.8090 (mp0) outliers start: 21 outliers final: 13 residues processed: 216 average time/residue: 0.1047 time to fit residues: 30.1692 Evaluate side-chains 182 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 46 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: 8.9990 chunk 24 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 230 ASN G 44 HIS A 306 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 = 0.4059 r_free = 0.4059 target = 0.121042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.099054 restraints weight = 23047.161| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 4.44 r_work: 0.3552 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 8879 Z= 0.251 Angle : 0.794 15.310 12029 Z= 0.414 Chirality : 0.048 0.211 1376 Planarity : 0.005 0.045 1498 Dihedral : 5.863 55.882 1214 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 3.36 % Allowed : 16.16 % Favored : 80.48 % 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 aren not related in a simple way. whole: -0.25 (0.26), residues: 1085 helix: 1.18 (0.27), residues: 379 sheet: -0.65 (0.30), residues: 272 loop : -0.97 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 148 TYR 0.026 0.002 TYR S 178 PHE 0.012 0.002 PHE B 199 TRP 0.017 0.002 TRP R 184 HIS 0.004 0.002 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00578 ( 8873) covalent geometry : angle 0.77100 (12017) SS BOND : bond 0.02387 ( 6) SS BOND : angle 6.05244 ( 12) hydrogen bonds : bond 0.05613 ( 424) hydrogen bonds : angle 5.53778 ( 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 213 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.376 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 217 MET cc_start: 0.8586 (ptt) cc_final: 0.8273 (ptt) REVERT: B 220 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6705 (tt0) REVERT: B 262 MET cc_start: 0.7350 (mmm) cc_final: 0.6939 (mmm) REVERT: B 264 TYR cc_start: 0.7640 (m-80) cc_final: 0.7422 (m-10) REVERT: B 325 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8719 (mmm) REVERT: G 15 LEU cc_start: 0.9170 (tt) cc_final: 0.8969 (pp) REVERT: G 42 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7700 (pt0) REVERT: R 184 TRP cc_start: 0.6472 (m-90) cc_final: 0.6012 (m-90) REVERT: A 18 MET cc_start: 0.8274 (tpp) cc_final: 0.7597 (mmm) REVERT: A 25 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8130 (pt0) REVERT: A 225 VAL cc_start: 0.6019 (t) cc_final: 0.5785 (m) REVERT: A 333 GLN cc_start: 0.8272 (tp-100) cc_final: 0.7871 (tp-100) REVERT: A 337 ASP cc_start: 0.7780 (m-30) cc_final: 0.7162 (m-30) REVERT: S 82 GLN cc_start: 0.7464 (tp40) cc_final: 0.7023 (tp-100) REVERT: S 109 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7622 (m-30) REVERT: S 208 GLU cc_start: 0.8319 (mp0) cc_final: 0.8093 (mp0) outliers start: 32 outliers final: 23 residues processed: 194 average time/residue: 0.1132 time to fit residues: 29.3495 Evaluate side-chains 192 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 220 GLN 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 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 275 MET 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 281 SER Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 344 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: 0.9990 chunk 87 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 220 GLN G 44 HIS A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.121459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.099459 restraints weight = 22890.901| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 4.42 r_work: 0.3647 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8879 Z= 0.147 Angle : 0.694 12.993 12029 Z= 0.364 Chirality : 0.045 0.228 1376 Planarity : 0.004 0.046 1498 Dihedral : 5.626 54.211 1214 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 2.73 % Allowed : 17.73 % Favored : 79.54 % 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 aren not related in a simple way. whole: 0.03 (0.26), residues: 1085 helix: 1.64 (0.27), residues: 372 sheet: -0.43 (0.30), residues: 258 loop : -1.04 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 148 TYR 0.026 0.002 TYR S 178 PHE 0.014 0.001 PHE R 288 TRP 0.016 0.002 TRP B 339 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8873) covalent geometry : angle 0.67682 (12017) SS BOND : bond 0.01757 ( 6) SS BOND : angle 4.90957 ( 12) hydrogen bonds : bond 0.04757 ( 424) hydrogen bonds : angle 5.26226 ( 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 212 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.366 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: B 91 HIS cc_start: 0.7890 (m-70) cc_final: 0.7584 (m-70) REVERT: B 175 GLN cc_start: 0.8672 (mm110) cc_final: 0.8238 (mp10) REVERT: B 217 MET cc_start: 0.8595 (ptt) cc_final: 0.8268 (ptt) REVERT: B 264 TYR cc_start: 0.7514 (m-80) cc_final: 0.7250 (m-10) REVERT: B 325 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.7901 (ptp) REVERT: G 42 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7721 (pt0) REVERT: R 184 TRP cc_start: 0.6325 (m-90) cc_final: 0.5853 (m-90) REVERT: A 25 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8143 (pt0) REVERT: A 318 GLU cc_start: 0.8456 (pm20) cc_final: 0.8007 (pm20) REVERT: A 333 GLN cc_start: 0.8323 (tp-100) cc_final: 0.8038 (tp-100) REVERT: S 34 MET cc_start: 0.5285 (mmp) cc_final: 0.4938 (mmm) REVERT: S 82 GLN cc_start: 0.7874 (tp40) cc_final: 0.7425 (tp-100) REVERT: S 93 MET cc_start: 0.8902 (ptm) cc_final: 0.8523 (tmm) REVERT: S 222 GLU cc_start: 0.8555 (tp30) cc_final: 0.8344 (tm-30) outliers start: 26 outliers final: 17 residues processed: 197 average time/residue: 0.1116 time to fit residues: 29.5141 Evaluate side-chains 184 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 128 THR 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 64 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 141 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 254 CYS Chi-restraints excluded: chain A residue 281 SER 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: 5.9990 chunk 43 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 71 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 79 optimal weight: 0.1980 chunk 3 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN G 44 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.127129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.105172 restraints weight = 22380.350| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 4.48 r_work: 0.3670 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8879 Z= 0.140 Angle : 0.712 15.633 12029 Z= 0.365 Chirality : 0.045 0.200 1376 Planarity : 0.004 0.052 1498 Dihedral : 5.499 54.203 1214 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 2.73 % Allowed : 19.62 % Favored : 77.65 % 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 aren not related in a simple way. whole: 0.02 (0.26), residues: 1085 helix: 1.50 (0.27), residues: 376 sheet: -0.33 (0.32), residues: 250 loop : -1.01 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 148 TYR 0.022 0.001 TYR S 103 PHE 0.025 0.001 PHE R 93 TRP 0.016 0.001 TRP B 339 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8873) covalent geometry : angle 0.69624 (12017) SS BOND : bond 0.01729 ( 6) SS BOND : angle 4.72795 ( 12) hydrogen bonds : bond 0.04495 ( 424) hydrogen bonds : angle 5.17143 ( 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 202 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.363 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 37 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7278 (mp) REVERT: B 91 HIS cc_start: 0.7751 (m-70) cc_final: 0.7254 (m-70) REVERT: B 175 GLN cc_start: 0.8696 (mm110) cc_final: 0.8248 (mp10) REVERT: B 259 GLN cc_start: 0.7272 (pp30) cc_final: 0.7046 (pp30) REVERT: B 262 MET cc_start: 0.7961 (mmm) cc_final: 0.7331 (mmm) REVERT: B 325 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8376 (mmm) REVERT: B 337 LYS cc_start: 0.7576 (mttm) cc_final: 0.7359 (mttp) REVERT: G 15 LEU cc_start: 0.9142 (tt) cc_final: 0.8927 (pp) REVERT: G 21 MET cc_start: 0.9507 (mpp) cc_final: 0.9281 (mpp) REVERT: G 42 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7748 (pt0) REVERT: G 46 LYS cc_start: 0.9548 (tppp) cc_final: 0.9072 (tppt) REVERT: A 25 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8125 (pt0) REVERT: A 46 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6928 (mtmm) REVERT: A 314 LYS cc_start: 0.9044 (mppt) cc_final: 0.8734 (mttm) REVERT: A 318 GLU cc_start: 0.8420 (pm20) cc_final: 0.8069 (pm20) REVERT: A 333 GLN cc_start: 0.8318 (tp-100) cc_final: 0.8028 (tp-100) REVERT: A 341 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8196 (t0) REVERT: S 34 MET cc_start: 0.5238 (mmp) cc_final: 0.4844 (mmm) REVERT: S 38 ARG cc_start: 0.7464 (ptt180) cc_final: 0.7026 (ptt180) REVERT: S 67 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7417 (tmm-80) REVERT: S 82 GLN cc_start: 0.7849 (tp40) cc_final: 0.7424 (tp-100) REVERT: S 93 MET cc_start: 0.8817 (ptm) cc_final: 0.8500 (tmm) REVERT: S 208 GLU cc_start: 0.7763 (mp0) cc_final: 0.7532 (mp0) REVERT: S 223 TYR cc_start: 0.7709 (m-80) cc_final: 0.7402 (m-80) outliers start: 26 outliers final: 18 residues processed: 193 average time/residue: 0.1176 time to fit residues: 29.9524 Evaluate side-chains 187 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 149 CYS 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 B residue 339 TRP Chi-restraints excluded: chain R residue 22 ILE 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 286 LYS Chi-restraints excluded: chain A residue 46 LYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 266 HIS B 295 ASN G 44 HIS R 30 ASN A 304 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.120284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.098298 restraints weight = 22806.329| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 4.38 r_work: 0.3582 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.4554 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= 0.169 Angle : 0.723 13.520 12029 Z= 0.374 Chirality : 0.045 0.178 1376 Planarity : 0.004 0.054 1498 Dihedral : 5.493 53.486 1214 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 4.09 % Allowed : 19.41 % Favored : 76.50 % 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 aren not related in a simple way. whole: -0.07 (0.26), residues: 1085 helix: 1.38 (0.27), residues: 375 sheet: -0.43 (0.30), residues: 268 loop : -0.98 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 148 TYR 0.026 0.002 TYR S 178 PHE 0.013 0.002 PHE R 288 TRP 0.013 0.002 TRP B 82 HIS 0.007 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8873) covalent geometry : angle 0.70595 (12017) SS BOND : bond 0.01895 ( 6) SS BOND : angle 4.99109 ( 12) hydrogen bonds : bond 0.04702 ( 424) hydrogen bonds : angle 5.16792 ( 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 203 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.360 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: B 37 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7203 (mp) REVERT: B 91 HIS cc_start: 0.7989 (m-70) cc_final: 0.7621 (m-70) REVERT: B 175 GLN cc_start: 0.8718 (mm110) cc_final: 0.8290 (mp10) REVERT: B 264 TYR cc_start: 0.7619 (m-80) cc_final: 0.7342 (m-10) REVERT: B 325 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8442 (mmm) REVERT: B 337 LYS cc_start: 0.7537 (mttm) cc_final: 0.7333 (mttp) REVERT: G 15 LEU cc_start: 0.9090 (tt) cc_final: 0.8852 (pp) REVERT: G 42 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7825 (pt0) REVERT: G 46 LYS cc_start: 0.9566 (tppp) cc_final: 0.9123 (tppt) REVERT: R 275 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6618 (tmm) REVERT: A 25 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8077 (pt0) REVERT: A 214 CYS cc_start: 0.9220 (m) cc_final: 0.8853 (t) REVERT: A 314 LYS cc_start: 0.9061 (mppt) cc_final: 0.8763 (mttm) REVERT: A 318 GLU cc_start: 0.8406 (pm20) cc_final: 0.8017 (pm20) REVERT: A 333 GLN cc_start: 0.8278 (tp-100) cc_final: 0.7929 (tp-100) REVERT: A 351 CYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6797 (m) REVERT: S 34 MET cc_start: 0.5446 (mmp) cc_final: 0.5096 (mmm) REVERT: S 82 GLN cc_start: 0.7822 (tp40) cc_final: 0.7319 (tp40) REVERT: S 93 MET cc_start: 0.8802 (ptm) cc_final: 0.8493 (tmm) REVERT: S 208 GLU cc_start: 0.8263 (mp0) cc_final: 0.7826 (mp0) REVERT: S 210 GLU cc_start: 0.7372 (pm20) cc_final: 0.6949 (pm20) outliers start: 39 outliers final: 28 residues processed: 186 average time/residue: 0.1120 time to fit residues: 27.8210 Evaluate side-chains 189 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 128 THR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE 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 22 ILE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE 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 165 CYS Chi-restraints excluded: chain R residue 275 MET 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 343 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 chunk 55 optimal weight: 0.0670 chunk 57 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.126583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.104807 restraints weight = 22638.007| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 4.41 r_work: 0.3674 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8879 Z= 0.149 Angle : 0.718 12.484 12029 Z= 0.375 Chirality : 0.045 0.185 1376 Planarity : 0.004 0.061 1498 Dihedral : 5.451 52.999 1214 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.58 % Rotamer: Outliers : 3.46 % Allowed : 20.67 % 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 aren not related in a simple way. whole: 0.02 (0.26), residues: 1085 helix: 1.59 (0.27), residues: 373 sheet: -0.48 (0.30), residues: 268 loop : -0.97 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 148 TYR 0.020 0.002 TYR S 103 PHE 0.025 0.001 PHE A 250 TRP 0.036 0.002 TRP R 184 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8873) covalent geometry : angle 0.70351 (12017) SS BOND : bond 0.01798 ( 6) SS BOND : angle 4.63116 ( 12) hydrogen bonds : bond 0.04549 ( 424) hydrogen bonds : angle 5.13542 ( 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 195 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.350 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 37 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7191 (mp) REVERT: B 75 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8326 (mt0) REVERT: B 91 HIS cc_start: 0.7944 (m-70) cc_final: 0.7376 (m-70) REVERT: B 175 GLN cc_start: 0.8710 (mm110) cc_final: 0.8307 (mp10) REVERT: B 264 TYR cc_start: 0.7539 (m-80) cc_final: 0.7255 (m-10) REVERT: B 325 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8379 (mmm) REVERT: G 15 LEU cc_start: 0.9110 (tt) cc_final: 0.8884 (pp) REVERT: G 42 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7847 (pt0) REVERT: G 46 LYS cc_start: 0.9529 (tppp) cc_final: 0.9106 (tppt) REVERT: A 25 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8087 (pt0) REVERT: A 214 CYS cc_start: 0.9216 (m) cc_final: 0.8793 (t) REVERT: A 307 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8243 (t80) REVERT: A 314 LYS cc_start: 0.9036 (mppt) cc_final: 0.8743 (mttm) REVERT: A 318 GLU cc_start: 0.8400 (pm20) cc_final: 0.8108 (pm20) REVERT: A 333 GLN cc_start: 0.8395 (tp-100) cc_final: 0.8061 (tp-100) REVERT: A 351 CYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7059 (m) REVERT: S 34 MET cc_start: 0.5433 (mmp) cc_final: 0.5017 (mmm) REVERT: S 82 GLN cc_start: 0.7800 (tp40) cc_final: 0.7303 (tp40) REVERT: S 208 GLU cc_start: 0.8306 (mp0) cc_final: 0.7850 (mp0) REVERT: S 210 GLU cc_start: 0.7423 (pm20) cc_final: 0.7081 (pm20) REVERT: S 222 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7957 (mm-30) outliers start: 33 outliers final: 26 residues processed: 181 average time/residue: 0.1179 time to fit residues: 28.2586 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 : 0.342 ------------------------------------------------------------------------------- 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 128 THR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE 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 22 ILE 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 114 LEU Chi-restraints excluded: chain R residue 165 CYS 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 307 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 42 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 77 optimal weight: 0.0170 chunk 64 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 45 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS A 22 ASN ** 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 = 0.4193 r_free = 0.4193 target = 0.128662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.106846 restraints weight = 22343.799| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 4.42 r_work: 0.3652 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8879 Z= 0.137 Angle : 0.744 18.455 12029 Z= 0.380 Chirality : 0.045 0.233 1376 Planarity : 0.004 0.060 1498 Dihedral : 5.308 49.981 1214 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 3.25 % Allowed : 21.41 % Favored : 75.34 % 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 aren not related in a simple way. whole: 0.11 (0.26), residues: 1085 helix: 1.75 (0.27), residues: 373 sheet: -0.44 (0.31), residues: 262 loop : -1.01 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 148 TYR 0.020 0.002 TYR S 103 PHE 0.010 0.001 PHE S 165 TRP 0.035 0.002 TRP R 184 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8873) covalent geometry : angle 0.73207 (12017) SS BOND : bond 0.01631 ( 6) SS BOND : angle 4.19708 ( 12) hydrogen bonds : bond 0.04293 ( 424) hydrogen bonds : angle 5.10385 ( 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 202 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.421 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 75 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8359 (mt0) REVERT: B 91 HIS cc_start: 0.7751 (m-70) cc_final: 0.7228 (m-70) REVERT: B 175 GLN cc_start: 0.8751 (mm110) cc_final: 0.8341 (mp10) REVERT: B 264 TYR cc_start: 0.7456 (m-80) cc_final: 0.7182 (m-10) REVERT: B 325 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8323 (mmm) REVERT: G 15 LEU cc_start: 0.9085 (tt) cc_final: 0.8851 (pp) REVERT: G 42 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7830 (pt0) REVERT: G 46 LYS cc_start: 0.9543 (tppp) cc_final: 0.9096 (tppt) REVERT: R 66 MET cc_start: 0.8007 (tmm) cc_final: 0.7718 (ppp) REVERT: A 25 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8175 (pt0) REVERT: A 214 CYS cc_start: 0.9223 (m) cc_final: 0.8813 (t) REVERT: A 307 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8314 (t80) REVERT: A 314 LYS cc_start: 0.9070 (mppt) cc_final: 0.8765 (mttm) REVERT: A 318 GLU cc_start: 0.8358 (pm20) cc_final: 0.8082 (pm20) REVERT: A 333 GLN cc_start: 0.8353 (tp-100) cc_final: 0.8028 (tp-100) REVERT: A 351 CYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6973 (m) REVERT: S 34 MET cc_start: 0.5455 (mmp) cc_final: 0.5029 (mmm) REVERT: S 82 GLN cc_start: 0.7772 (tp40) cc_final: 0.7333 (tp40) REVERT: S 93 MET cc_start: 0.8794 (tmm) cc_final: 0.8507 (ppp) REVERT: S 208 GLU cc_start: 0.8344 (mp0) cc_final: 0.7927 (mp0) REVERT: S 210 GLU cc_start: 0.7374 (pm20) cc_final: 0.7165 (pm20) outliers start: 31 outliers final: 25 residues processed: 186 average time/residue: 0.1106 time to fit residues: 27.1367 Evaluate side-chains 188 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 128 THR 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 22 ILE 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 114 LEU Chi-restraints excluded: chain R residue 165 CYS 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 254 CYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 307 PHE 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 174 GLN 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: 0.5980 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 13 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.125935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.104053 restraints weight = 22610.415| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 4.40 r_work: 0.3612 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8879 Z= 0.170 Angle : 0.770 13.239 12029 Z= 0.393 Chirality : 0.046 0.210 1376 Planarity : 0.004 0.058 1498 Dihedral : 5.421 50.274 1214 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.21 % Rotamer: Outliers : 3.36 % Allowed : 21.30 % Favored : 75.34 % 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 aren not related in a simple way. whole: -0.03 (0.26), residues: 1085 helix: 1.59 (0.27), residues: 376 sheet: -0.59 (0.29), residues: 278 loop : -1.02 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 148 TYR 0.037 0.002 TYR S 178 PHE 0.021 0.002 PHE A 250 TRP 0.030 0.002 TRP B 211 HIS 0.007 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8873) covalent geometry : angle 0.75576 (12017) SS BOND : bond 0.01816 ( 6) SS BOND : angle 4.75269 ( 12) hydrogen bonds : bond 0.04560 ( 424) hydrogen bonds : angle 5.18052 ( 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 197 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.376 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: B 15 LYS cc_start: 0.8549 (pttm) cc_final: 0.8317 (pttm) REVERT: B 37 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.7028 (mp) REVERT: B 75 GLN cc_start: 0.8690 (mt0) cc_final: 0.8353 (mt0) REVERT: B 91 HIS cc_start: 0.7904 (m-70) cc_final: 0.7302 (m90) REVERT: B 175 GLN cc_start: 0.8756 (mm110) cc_final: 0.8404 (mp10) REVERT: B 264 TYR cc_start: 0.7612 (m-80) cc_final: 0.7283 (m-10) REVERT: B 325 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8438 (mmm) REVERT: G 15 LEU cc_start: 0.9127 (tt) cc_final: 0.8886 (pp) REVERT: G 42 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7838 (pt0) REVERT: G 46 LYS cc_start: 0.9550 (tppp) cc_final: 0.9140 (tppt) REVERT: R 90 MET cc_start: 0.3064 (mmt) cc_final: 0.2859 (mmt) REVERT: R 275 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6621 (tmm) REVERT: A 25 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8056 (pt0) REVERT: A 307 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8174 (t80) REVERT: A 314 LYS cc_start: 0.9070 (mppt) cc_final: 0.8761 (mttp) REVERT: A 318 GLU cc_start: 0.8357 (pm20) cc_final: 0.8092 (pm20) REVERT: A 333 GLN cc_start: 0.8350 (tp-100) cc_final: 0.8043 (tp-100) REVERT: A 351 CYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6653 (m) REVERT: S 34 MET cc_start: 0.5597 (mmp) cc_final: 0.5212 (mmm) REVERT: S 82 GLN cc_start: 0.7773 (tp40) cc_final: 0.7504 (mm-40) REVERT: S 93 MET cc_start: 0.8631 (tmm) cc_final: 0.8408 (ppp) REVERT: S 171 GLN cc_start: 0.8681 (mp10) cc_final: 0.8344 (mp10) REVERT: S 208 GLU cc_start: 0.8299 (mp0) cc_final: 0.7826 (mp0) REVERT: S 210 GLU cc_start: 0.7326 (pm20) cc_final: 0.7090 (pm20) outliers start: 32 outliers final: 26 residues processed: 182 average time/residue: 0.1140 time to fit residues: 27.6478 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 : 0.373 ------------------------------------------------------------------------------- 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 128 THR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE 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 22 ILE 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 114 LEU Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 275 MET 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 307 PHE 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 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: 0.8980 chunk 50 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 78 optimal weight: 0.0030 chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 72 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS ** A 269 ASN ** 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 = 0.4200 r_free = 0.4200 target = 0.128923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.107105 restraints weight = 22345.056| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 4.39 r_work: 0.3668 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8879 Z= 0.146 Angle : 0.773 14.365 12029 Z= 0.398 Chirality : 0.046 0.246 1376 Planarity : 0.004 0.059 1498 Dihedral : 5.309 49.218 1214 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.48 % Rotamer: Outliers : 2.62 % Allowed : 22.98 % 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 aren not related in a simple way. whole: -0.05 (0.26), residues: 1085 helix: 1.52 (0.27), residues: 381 sheet: -0.59 (0.30), residues: 276 loop : -1.01 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 148 TYR 0.023 0.002 TYR A 302 PHE 0.025 0.001 PHE S 32 TRP 0.029 0.002 TRP R 184 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8873) covalent geometry : angle 0.76294 (12017) SS BOND : bond 0.01526 ( 6) SS BOND : angle 4.04934 ( 12) hydrogen bonds : bond 0.04347 ( 424) hydrogen bonds : angle 5.22990 ( 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 195 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.365 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 37 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6890 (mp) REVERT: B 57 LYS cc_start: 0.8415 (mttp) cc_final: 0.8029 (ptpp) REVERT: B 91 HIS cc_start: 0.7877 (m-70) cc_final: 0.7329 (m-70) REVERT: B 138 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7788 (mm-30) REVERT: B 175 GLN cc_start: 0.8706 (mm110) cc_final: 0.8327 (mp10) REVERT: B 264 TYR cc_start: 0.7407 (m-80) cc_final: 0.7170 (m-10) REVERT: B 325 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8345 (mmm) REVERT: G 15 LEU cc_start: 0.9143 (tt) cc_final: 0.8899 (pp) REVERT: G 42 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7978 (pt0) REVERT: G 46 LYS cc_start: 0.9490 (tppp) cc_final: 0.9082 (tppt) REVERT: R 66 MET cc_start: 0.8035 (tmm) cc_final: 0.7684 (ppp) REVERT: A 25 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8007 (pt0) REVERT: A 250 PHE cc_start: 0.8744 (t80) cc_final: 0.8519 (t80) REVERT: A 307 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.7977 (t80) REVERT: A 308 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8752 (mm-30) REVERT: A 314 LYS cc_start: 0.9040 (mppt) cc_final: 0.8667 (mttp) REVERT: A 333 GLN cc_start: 0.8249 (tp-100) cc_final: 0.7997 (tp-100) REVERT: A 351 CYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6585 (m) REVERT: S 34 MET cc_start: 0.5542 (mmp) cc_final: 0.5075 (mmm) REVERT: S 82 GLN cc_start: 0.7739 (tp40) cc_final: 0.7298 (tp40) REVERT: S 93 MET cc_start: 0.8593 (tmm) cc_final: 0.8371 (ppp) REVERT: S 171 GLN cc_start: 0.8650 (mp10) cc_final: 0.8336 (mp10) REVERT: S 208 GLU cc_start: 0.8397 (mp0) cc_final: 0.7884 (mp0) REVERT: S 210 GLU cc_start: 0.7349 (pm20) cc_final: 0.7106 (pm20) outliers start: 25 outliers final: 20 residues processed: 182 average time/residue: 0.1030 time to fit residues: 25.2383 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 : 0.367 ------------------------------------------------------------------------------- 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 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 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 165 CYS Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 307 PHE 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 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: 0.9990 chunk 61 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** 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 = 0.4172 r_free = 0.4172 target = 0.126897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.105363 restraints weight = 22431.036| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 4.35 r_work: 0.3641 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8879 Z= 0.164 Angle : 0.796 13.792 12029 Z= 0.405 Chirality : 0.046 0.219 1376 Planarity : 0.004 0.063 1498 Dihedral : 5.255 45.541 1214 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.48 % Rotamer: Outliers : 2.62 % Allowed : 23.08 % Favored : 74.29 % 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 aren not related in a simple way. whole: -0.08 (0.26), residues: 1085 helix: 1.56 (0.27), residues: 376 sheet: -0.59 (0.30), residues: 278 loop : -1.08 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 148 TYR 0.030 0.002 TYR S 178 PHE 0.020 0.002 PHE S 32 TRP 0.025 0.002 TRP B 211 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8873) covalent geometry : angle 0.78496 (12017) SS BOND : bond 0.01551 ( 6) SS BOND : angle 4.16598 ( 12) hydrogen bonds : bond 0.04472 ( 424) hydrogen bonds : angle 5.22189 ( 1185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2861.51 seconds wall clock time: 49 minutes 48.40 seconds (2988.40 seconds total)