Starting phenix.real_space_refine on Sat Jul 26 12:46:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yh2_39279/07_2025/8yh2_39279.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yh2_39279/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8yh2_39279/07_2025/8yh2_39279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yh2_39279/07_2025/8yh2_39279.map" model { file = "/net/cci-nas-00/data/ceres_data/8yh2_39279/07_2025/8yh2_39279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yh2_39279/07_2025/8yh2_39279.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.47, per 1000 atoms: 0.63 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: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.01 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: 2.35 Time building geometry restraints manager: 2.75 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: 0.330 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.650 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.550 ------------------------------------------------------------------------------- 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 : 10.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.001 TRP R 35 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE B 234 TYR 0.017 0.001 TYR S 178 ARG 0.004 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.19777 ( 424) hydrogen bonds : angle 7.17764 ( 1185) SS BOND : bond 0.01835 ( 6) SS BOND : angle 3.84553 ( 12) covalent geometry : bond 0.00423 ( 8873) covalent geometry : angle 0.62865 (12017) *********************** 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 : 0.956 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: 0.2559 time to fit residues: 90.1907 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 : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 45 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.127643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.105847 restraints weight = 22330.206| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 4.37 r_work: 0.3658 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 8879 Z= 0.184 Angle : 0.770 12.493 12029 Z= 0.402 Chirality : 0.047 0.231 1376 Planarity : 0.005 0.057 1498 Dihedral : 5.762 59.448 1214 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.94 % Rotamer: Outliers : 1.99 % Allowed : 12.17 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1085 helix: 1.58 (0.27), residues: 375 sheet: -0.59 (0.30), residues: 268 loop : -0.97 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 184 HIS 0.004 0.001 HIS A 322 PHE 0.022 0.002 PHE R 167 TYR 0.012 0.002 TYR A 287 ARG 0.006 0.001 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.05466 ( 424) hydrogen bonds : angle 5.70169 ( 1185) SS BOND : bond 0.01677 ( 6) SS BOND : angle 5.97079 ( 12) covalent geometry : bond 0.00421 ( 8873) covalent geometry : angle 0.74679 (12017) *********************** 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 231 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 212 time to evaluate : 1.091 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 215 GLU cc_start: 0.9284 (mp0) cc_final: 0.8931 (mp0) REVERT: B 325 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8632 (mmm) REVERT: G 15 LEU cc_start: 0.9168 (tt) cc_final: 0.8958 (pp) REVERT: G 42 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7594 (pt0) REVERT: G 44 HIS cc_start: 0.8128 (m-70) cc_final: 0.7304 (t70) REVERT: G 47 GLU cc_start: 0.8190 (tp30) cc_final: 0.7981 (tm-30) REVERT: R 128 TRP cc_start: 0.7454 (m100) cc_final: 0.7136 (m100) REVERT: A 18 MET cc_start: 0.8206 (tpp) cc_final: 0.7622 (mmm) REVERT: A 22 ASN cc_start: 0.7347 (m110) cc_final: 0.6865 (m-40) REVERT: A 256 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8242 (p0) REVERT: A 269 ASN cc_start: 0.6288 (p0) cc_final: 0.5814 (p0) REVERT: A 308 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8842 (mm-30) REVERT: A 333 GLN cc_start: 0.7960 (tp-100) cc_final: 0.7636 (tp-100) REVERT: A 337 ASP cc_start: 0.7524 (m-30) cc_final: 0.6984 (m-30) REVERT: A 349 LYS cc_start: 0.8125 (ttpt) cc_final: 0.7923 (ttpp) REVERT: S 82 GLN cc_start: 0.7679 (tp40) cc_final: 0.7357 (tp-100) REVERT: S 128 MET cc_start: 0.5297 (OUTLIER) cc_final: 0.4935 (mtp) REVERT: S 148 ARG cc_start: 0.7879 (mmm-85) cc_final: 0.7248 (mmm-85) REVERT: S 208 GLU cc_start: 0.8365 (mp0) cc_final: 0.8069 (mp0) outliers start: 19 outliers final: 11 residues processed: 220 average time/residue: 0.2502 time to fit residues: 73.2469 Evaluate side-chains 189 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 35 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 230 ASN G 44 HIS ** S 219 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 = 0.4167 r_free = 0.4167 target = 0.128303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.107331 restraints weight = 22591.969| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 4.22 r_work: 0.3672 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8879 Z= 0.147 Angle : 0.700 11.842 12029 Z= 0.365 Chirality : 0.045 0.214 1376 Planarity : 0.004 0.042 1498 Dihedral : 5.598 55.507 1214 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.50 % Rotamer: Outliers : 2.62 % Allowed : 15.53 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1085 helix: 1.63 (0.27), residues: 375 sheet: -0.44 (0.30), residues: 264 loop : -0.93 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 184 HIS 0.004 0.001 HIS A 322 PHE 0.014 0.001 PHE A 189 TYR 0.025 0.002 TYR S 178 ARG 0.007 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04771 ( 424) hydrogen bonds : angle 5.29177 ( 1185) SS BOND : bond 0.01616 ( 6) SS BOND : angle 4.76749 ( 12) covalent geometry : bond 0.00324 ( 8873) covalent geometry : angle 0.68434 (12017) *********************** 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 218 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 1.037 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: 0.7878 (m-70) cc_final: 0.7510 (m-70) REVERT: B 175 GLN cc_start: 0.8645 (mm110) cc_final: 0.8288 (mp10) REVERT: B 259 GLN cc_start: 0.6919 (pp30) cc_final: 0.6449 (pp30) REVERT: B 264 TYR cc_start: 0.7320 (m-80) cc_final: 0.7019 (m-10) REVERT: B 325 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8454 (mmm) REVERT: G 42 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7671 (pt0) REVERT: G 44 HIS cc_start: 0.8045 (m170) cc_final: 0.7524 (t70) REVERT: A 18 MET cc_start: 0.8150 (tpp) cc_final: 0.7547 (mmm) REVERT: A 22 ASN cc_start: 0.7503 (m110) cc_final: 0.6948 (m-40) REVERT: A 269 ASN cc_start: 0.6080 (p0) cc_final: 0.5511 (p0) REVERT: A 287 TYR cc_start: 0.5913 (t80) cc_final: 0.5333 (t80) REVERT: A 314 LYS cc_start: 0.9008 (mppt) cc_final: 0.8788 (mttm) REVERT: A 333 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7821 (tp-100) REVERT: A 337 ASP cc_start: 0.7794 (m-30) cc_final: 0.7194 (m-30) REVERT: S 34 MET cc_start: 0.5301 (mmp) cc_final: 0.4983 (mmm) REVERT: S 50 TYR cc_start: 0.8258 (t80) cc_final: 0.8000 (t80) REVERT: S 82 GLN cc_start: 0.7673 (tp40) cc_final: 0.7290 (tp40) REVERT: S 128 MET cc_start: 0.5135 (OUTLIER) cc_final: 0.4722 (mtp) REVERT: S 148 ARG cc_start: 0.7887 (mmm-85) cc_final: 0.7261 (mmm-85) REVERT: S 208 GLU cc_start: 0.8423 (mp0) cc_final: 0.7970 (mp0) REVERT: S 210 GLU cc_start: 0.7517 (pm20) cc_final: 0.7146 (pm20) outliers start: 25 outliers final: 13 residues processed: 202 average time/residue: 0.2348 time to fit residues: 63.1972 Evaluate side-chains 188 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 65 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN ** S 219 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 = 0.4008 r_free = 0.4008 target = 0.118238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.096421 restraints weight = 23078.647| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 4.28 r_work: 0.3576 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 8879 Z= 0.215 Angle : 0.751 14.214 12029 Z= 0.392 Chirality : 0.047 0.247 1376 Planarity : 0.005 0.050 1498 Dihedral : 5.651 54.601 1214 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 3.15 % Allowed : 17.63 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.26), residues: 1085 helix: 1.28 (0.26), residues: 381 sheet: -0.37 (0.31), residues: 261 loop : -1.02 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.019 0.002 PHE R 80 TYR 0.015 0.002 TYR A 302 ARG 0.006 0.000 ARG S 206 Details of bonding type rmsd hydrogen bonds : bond 0.05200 ( 424) hydrogen bonds : angle 5.29520 ( 1185) SS BOND : bond 0.02079 ( 6) SS BOND : angle 5.51377 ( 12) covalent geometry : bond 0.00493 ( 8873) covalent geometry : angle 0.73108 (12017) *********************** 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 204 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.949 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 59 TYR cc_start: 0.7975 (m-80) cc_final: 0.7627 (m-80) REVERT: B 75 GLN cc_start: 0.8497 (tt0) cc_final: 0.8181 (tt0) REVERT: B 91 HIS cc_start: 0.8027 (m-70) cc_final: 0.7634 (m-70) REVERT: B 175 GLN cc_start: 0.8647 (mm110) cc_final: 0.8268 (mp10) REVERT: B 262 MET cc_start: 0.7501 (mmm) cc_final: 0.7174 (mmm) REVERT: B 325 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8217 (ptp) REVERT: G 42 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7723 (pt0) REVERT: G 44 HIS cc_start: 0.8222 (m170) cc_final: 0.7486 (t70) REVERT: G 47 GLU cc_start: 0.8373 (tp30) cc_final: 0.7509 (tm-30) REVERT: R 99 MET cc_start: 0.7519 (mmt) cc_final: 0.7152 (tpp) REVERT: A 18 MET cc_start: 0.8273 (tpp) cc_final: 0.7957 (tpp) REVERT: A 25 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8111 (pt0) REVERT: A 314 LYS cc_start: 0.9108 (mppt) cc_final: 0.8857 (mttm) REVERT: A 318 GLU cc_start: 0.8287 (pm20) cc_final: 0.7921 (pm20) REVERT: A 333 GLN cc_start: 0.8281 (tp-100) cc_final: 0.7962 (tp-100) REVERT: S 34 MET cc_start: 0.5565 (mmp) cc_final: 0.5155 (mmm) REVERT: S 38 ARG cc_start: 0.7595 (ptt180) cc_final: 0.7230 (ptt180) REVERT: S 82 GLN cc_start: 0.7476 (tp40) cc_final: 0.6996 (tp-100) REVERT: S 206 ARG cc_start: 0.8888 (mmp80) cc_final: 0.8620 (mmp80) REVERT: S 208 GLU cc_start: 0.8333 (mp0) cc_final: 0.7948 (mp0) REVERT: S 210 GLU cc_start: 0.7402 (pm20) cc_final: 0.6936 (pm20) outliers start: 30 outliers final: 25 residues processed: 188 average time/residue: 0.2437 time to fit residues: 60.5180 Evaluate side-chains 194 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 G residue 58 GLU 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 112 VAL Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 275 MET Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 343 ILE 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 72 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 B 266 HIS B 295 ASN A 22 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4060 r_free = 0.4060 target = 0.121308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.099585 restraints weight = 22826.003| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 4.30 r_work: 0.3643 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8879 Z= 0.146 Angle : 0.709 14.677 12029 Z= 0.364 Chirality : 0.045 0.194 1376 Planarity : 0.004 0.056 1498 Dihedral : 5.490 52.509 1214 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.85 % Rotamer: Outliers : 3.15 % Allowed : 18.89 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1085 helix: 1.60 (0.27), residues: 376 sheet: -0.37 (0.31), residues: 262 loop : -1.01 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 184 HIS 0.005 0.001 HIS B 225 PHE 0.016 0.002 PHE R 288 TYR 0.026 0.002 TYR S 178 ARG 0.007 0.000 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.04643 ( 424) hydrogen bonds : angle 5.19758 ( 1185) SS BOND : bond 0.01687 ( 6) SS BOND : angle 4.70688 ( 12) covalent geometry : bond 0.00320 ( 8873) covalent geometry : angle 0.69369 (12017) *********************** 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: 30 poor density : 172 time to evaluate : 0.954 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: 0.7436 (OUTLIER) cc_final: 0.7193 (mp) REVERT: B 91 HIS cc_start: 0.7938 (m-70) cc_final: 0.7659 (m-70) REVERT: B 175 GLN cc_start: 0.8618 (mm110) cc_final: 0.8224 (mp10) REVERT: B 262 MET cc_start: 0.7272 (mmm) cc_final: 0.6958 (mmm) REVERT: B 325 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8106 (ptp) REVERT: G 42 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7799 (pt0) REVERT: G 44 HIS cc_start: 0.8186 (m170) cc_final: 0.7580 (t70) REVERT: G 46 LYS cc_start: 0.9025 (tppt) cc_final: 0.8824 (tppt) REVERT: G 47 GLU cc_start: 0.8218 (tp30) cc_final: 0.7860 (tp30) REVERT: R 176 MET cc_start: 0.5770 (OUTLIER) cc_final: 0.5562 (tmm) REVERT: A 18 MET cc_start: 0.8121 (tpp) cc_final: 0.7656 (tpp) REVERT: A 25 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8186 (pt0) REVERT: A 302 TYR cc_start: 0.8335 (t80) cc_final: 0.7883 (t80) REVERT: A 314 LYS cc_start: 0.9094 (mppt) cc_final: 0.8841 (mttm) REVERT: A 318 GLU cc_start: 0.8350 (pm20) cc_final: 0.8053 (pm20) REVERT: A 333 GLN cc_start: 0.8312 (tp-100) cc_final: 0.8018 (tp-100) REVERT: S 34 MET cc_start: 0.5539 (mmp) cc_final: 0.5112 (mmm) REVERT: S 38 ARG cc_start: 0.7534 (ptt180) cc_final: 0.7146 (ptt180) REVERT: S 67 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7408 (tmm-80) REVERT: S 82 GLN cc_start: 0.7828 (tp40) cc_final: 0.7435 (tp40) REVERT: S 93 MET cc_start: 0.8612 (tmm) cc_final: 0.8343 (ppp) REVERT: S 200 PHE cc_start: 0.4741 (m-10) cc_final: 0.4471 (m-10) REVERT: S 206 ARG cc_start: 0.8839 (mmp80) cc_final: 0.8534 (mmp80) REVERT: S 208 GLU cc_start: 0.8352 (mp0) cc_final: 0.8010 (mp0) REVERT: S 210 GLU cc_start: 0.7594 (pm20) cc_final: 0.7270 (pm20) outliers start: 30 outliers final: 21 residues processed: 187 average time/residue: 0.2572 time to fit residues: 63.3473 Evaluate side-chains 185 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 G residue 58 GLU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 176 MET Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain 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 49 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.120930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.099220 restraints weight = 22690.485| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 4.28 r_work: 0.3634 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8879 Z= 0.147 Angle : 0.704 12.638 12029 Z= 0.361 Chirality : 0.045 0.193 1376 Planarity : 0.004 0.061 1498 Dihedral : 5.439 52.797 1214 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.39 % Rotamer: Outliers : 3.25 % Allowed : 19.41 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1085 helix: 1.64 (0.27), residues: 375 sheet: -0.48 (0.30), residues: 266 loop : -1.01 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 184 HIS 0.005 0.001 HIS B 225 PHE 0.013 0.002 PHE R 288 TYR 0.026 0.002 TYR S 178 ARG 0.002 0.000 ARG S 206 Details of bonding type rmsd hydrogen bonds : bond 0.04558 ( 424) hydrogen bonds : angle 5.09002 ( 1185) SS BOND : bond 0.01773 ( 6) SS BOND : angle 4.52502 ( 12) covalent geometry : bond 0.00331 ( 8873) covalent geometry : angle 0.69016 (12017) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.962 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 15 LYS cc_start: 0.9025 (pttm) cc_final: 0.8673 (ptpp) REVERT: B 91 HIS cc_start: 0.7897 (m-70) cc_final: 0.7607 (m-70) REVERT: B 175 GLN cc_start: 0.8662 (mm110) cc_final: 0.8280 (mp10) REVERT: B 259 GLN cc_start: 0.6492 (pp30) cc_final: 0.6270 (pp30) REVERT: B 262 MET cc_start: 0.7484 (mmm) cc_final: 0.7204 (mmm) REVERT: B 325 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8389 (mmm) REVERT: G 42 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7886 (pt0) REVERT: G 44 HIS cc_start: 0.8341 (m170) cc_final: 0.7709 (t70) REVERT: G 47 GLU cc_start: 0.8297 (tp30) cc_final: 0.8056 (tp30) REVERT: A 25 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8174 (pt0) REVERT: A 214 CYS cc_start: 0.9259 (m) cc_final: 0.8894 (t) REVERT: A 304 GLN cc_start: 0.8443 (tt0) cc_final: 0.8220 (tt0) REVERT: A 314 LYS cc_start: 0.9088 (mppt) cc_final: 0.8779 (mttm) REVERT: A 318 GLU cc_start: 0.8340 (pm20) cc_final: 0.8042 (pm20) REVERT: A 333 GLN cc_start: 0.8299 (tp-100) cc_final: 0.8008 (tp-100) REVERT: A 351 CYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7096 (m) REVERT: S 34 MET cc_start: 0.5543 (mmp) cc_final: 0.5129 (mmm) REVERT: S 38 ARG cc_start: 0.7456 (ptt180) cc_final: 0.7026 (ptt180) REVERT: S 82 GLN cc_start: 0.7674 (tp40) cc_final: 0.7214 (tp-100) REVERT: S 93 MET cc_start: 0.8544 (tmm) cc_final: 0.8248 (ppp) REVERT: S 174 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7805 (mm-40) REVERT: S 206 ARG cc_start: 0.8894 (mmp80) cc_final: 0.8635 (mmp80) REVERT: S 208 GLU cc_start: 0.8333 (mp0) cc_final: 0.8024 (mp0) REVERT: S 210 GLU cc_start: 0.7658 (pm20) cc_final: 0.7347 (pm20) outliers start: 31 outliers final: 24 residues processed: 182 average time/residue: 0.2376 time to fit residues: 57.3363 Evaluate side-chains 184 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 G residue 58 GLU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 80 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 19 optimal weight: 0.0170 chunk 66 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 52 optimal weight: 0.0870 chunk 26 optimal weight: 3.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.122313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.100316 restraints weight = 22532.162| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 4.37 r_work: 0.3614 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.4730 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= 0.149 Angle : 0.713 11.461 12029 Z= 0.364 Chirality : 0.044 0.182 1376 Planarity : 0.004 0.059 1498 Dihedral : 5.319 49.588 1214 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.58 % Rotamer: Outliers : 3.04 % Allowed : 20.57 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1085 helix: 1.74 (0.27), residues: 378 sheet: -0.59 (0.30), residues: 275 loop : -1.02 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 184 HIS 0.005 0.001 HIS B 225 PHE 0.012 0.001 PHE S 200 TYR 0.026 0.002 TYR S 178 ARG 0.003 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 424) hydrogen bonds : angle 5.05102 ( 1185) SS BOND : bond 0.01704 ( 6) SS BOND : angle 4.32924 ( 12) covalent geometry : bond 0.00334 ( 8873) covalent geometry : angle 0.70003 (12017) *********************** 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 189 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.962 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: 0.7447 (OUTLIER) cc_final: 0.7186 (mp) REVERT: B 75 GLN cc_start: 0.8792 (mt0) cc_final: 0.8515 (mt0) REVERT: B 91 HIS cc_start: 0.7831 (m-70) cc_final: 0.7477 (m-70) REVERT: B 101 MET cc_start: 0.6520 (mpp) cc_final: 0.6302 (mpp) REVERT: B 138 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7878 (mm-30) REVERT: B 175 GLN cc_start: 0.8694 (mm110) cc_final: 0.8295 (mp10) REVERT: B 325 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8381 (mmm) REVERT: G 42 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7700 (pt0) REVERT: G 44 HIS cc_start: 0.8389 (m170) cc_final: 0.7682 (t70) REVERT: G 47 GLU cc_start: 0.8310 (tp30) cc_final: 0.8019 (tp30) REVERT: A 25 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8082 (pt0) REVERT: A 214 CYS cc_start: 0.9258 (m) cc_final: 0.8840 (t) REVERT: A 302 TYR cc_start: 0.8592 (t80) cc_final: 0.8051 (t80) REVERT: A 314 LYS cc_start: 0.9138 (mppt) cc_final: 0.8899 (mttp) REVERT: A 318 GLU cc_start: 0.8293 (pm20) cc_final: 0.7950 (pm20) REVERT: A 333 GLN cc_start: 0.8261 (tp-100) cc_final: 0.7991 (tp-100) REVERT: A 351 CYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6784 (m) REVERT: S 34 MET cc_start: 0.5464 (mmp) cc_final: 0.5075 (mmm) REVERT: S 82 GLN cc_start: 0.7784 (tp40) cc_final: 0.7339 (tp40) REVERT: S 93 MET cc_start: 0.8696 (tmm) cc_final: 0.8422 (ppp) REVERT: S 208 GLU cc_start: 0.8276 (mp0) cc_final: 0.7999 (mp0) REVERT: S 210 GLU cc_start: 0.7667 (pm20) cc_final: 0.7387 (pm20) outliers start: 29 outliers final: 25 residues processed: 178 average time/residue: 0.2440 time to fit residues: 57.1730 Evaluate side-chains 179 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 G residue 58 GLU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 101 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 85 optimal weight: 0.3980 chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.122304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.100354 restraints weight = 22771.279| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 4.41 r_work: 0.3671 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8879 Z= 0.151 Angle : 0.737 10.729 12029 Z= 0.377 Chirality : 0.045 0.210 1376 Planarity : 0.005 0.057 1498 Dihedral : 5.189 45.909 1214 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 3.15 % Allowed : 19.94 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1085 helix: 1.67 (0.27), residues: 384 sheet: -0.60 (0.30), residues: 270 loop : -1.07 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.007 0.001 HIS B 225 PHE 0.011 0.001 PHE S 200 TYR 0.027 0.002 TYR S 178 ARG 0.009 0.001 ARG S 206 Details of bonding type rmsd hydrogen bonds : bond 0.04500 ( 424) hydrogen bonds : angle 5.05360 ( 1185) SS BOND : bond 0.01635 ( 6) SS BOND : angle 4.06756 ( 12) covalent geometry : bond 0.00342 ( 8873) covalent geometry : angle 0.72612 (12017) *********************** 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 192 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 1.018 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: 0.7373 (OUTLIER) cc_final: 0.7110 (mp) REVERT: B 75 GLN cc_start: 0.8763 (mt0) cc_final: 0.8404 (mt0) REVERT: B 91 HIS cc_start: 0.7890 (m-70) cc_final: 0.7533 (m-70) REVERT: B 138 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7866 (mm-30) REVERT: B 175 GLN cc_start: 0.8745 (mm110) cc_final: 0.8382 (mp10) REVERT: B 262 MET cc_start: 0.7826 (mmm) cc_final: 0.7528 (mmm) REVERT: B 325 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8396 (mmm) REVERT: G 42 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7735 (pt0) REVERT: G 44 HIS cc_start: 0.8452 (m170) cc_final: 0.7799 (t70) REVERT: G 46 LYS cc_start: 0.9508 (tppp) cc_final: 0.9256 (tppt) REVERT: R 99 MET cc_start: 0.7462 (mmt) cc_final: 0.7259 (mmm) REVERT: A 25 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8094 (pt0) REVERT: A 214 CYS cc_start: 0.9226 (m) cc_final: 0.8808 (t) REVERT: A 314 LYS cc_start: 0.9116 (mppt) cc_final: 0.8884 (mttp) REVERT: A 318 GLU cc_start: 0.8326 (pm20) cc_final: 0.8032 (pm20) REVERT: A 333 GLN cc_start: 0.8256 (tp-100) cc_final: 0.7993 (tp-100) REVERT: A 351 CYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6832 (m) REVERT: S 34 MET cc_start: 0.5527 (mmp) cc_final: 0.5221 (mmm) REVERT: S 82 GLN cc_start: 0.7760 (tp40) cc_final: 0.7489 (mm-40) REVERT: S 93 MET cc_start: 0.8693 (tmm) cc_final: 0.8417 (ppp) REVERT: S 174 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7773 (mm-40) REVERT: S 208 GLU cc_start: 0.8255 (mp0) cc_final: 0.7998 (mp0) REVERT: S 210 GLU cc_start: 0.7738 (pm20) cc_final: 0.7391 (pm20) outliers start: 30 outliers final: 24 residues processed: 179 average time/residue: 0.2416 time to fit residues: 56.9724 Evaluate side-chains 183 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 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 43 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 187 VAL 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 4 optimal weight: 0.0470 chunk 107 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 90 optimal weight: 0.3980 chunk 3 optimal weight: 6.9990 overall best weight: 1.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.120569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.098627 restraints weight = 22789.229| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 4.40 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8879 Z= 0.178 Angle : 0.768 11.303 12029 Z= 0.392 Chirality : 0.045 0.208 1376 Planarity : 0.004 0.056 1498 Dihedral : 5.308 46.855 1214 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.58 % Rotamer: Outliers : 3.46 % Allowed : 20.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.26), residues: 1085 helix: 1.56 (0.27), residues: 386 sheet: -0.67 (0.29), residues: 275 loop : -1.10 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 184 HIS 0.007 0.001 HIS B 225 PHE 0.011 0.002 PHE S 200 TYR 0.030 0.002 TYR S 178 ARG 0.008 0.001 ARG S 206 Details of bonding type rmsd hydrogen bonds : bond 0.04668 ( 424) hydrogen bonds : angle 5.12233 ( 1185) SS BOND : bond 0.01722 ( 6) SS BOND : angle 4.21520 ( 12) covalent geometry : bond 0.00412 ( 8873) covalent geometry : angle 0.75658 (12017) *********************** 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: 33 poor density : 164 time to evaluate : 0.948 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 19 ARG cc_start: 0.8294 (mmm160) cc_final: 0.7952 (mmm160) REVERT: B 37 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.7021 (mp) REVERT: B 75 GLN cc_start: 0.8595 (mt0) cc_final: 0.8192 (mt0) REVERT: B 91 HIS cc_start: 0.7927 (m-70) cc_final: 0.7568 (m-70) REVERT: B 175 GLN cc_start: 0.8449 (mm110) cc_final: 0.8109 (mp10) REVERT: B 259 GLN cc_start: 0.6739 (pp30) cc_final: 0.6430 (pp30) REVERT: B 262 MET cc_start: 0.7741 (mmm) cc_final: 0.7380 (mmm) REVERT: B 325 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8141 (mmm) REVERT: G 42 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7786 (pt0) REVERT: G 44 HIS cc_start: 0.8318 (m170) cc_final: 0.7784 (t70) REVERT: G 46 LYS cc_start: 0.9558 (tppp) cc_final: 0.9193 (tppt) REVERT: A 20 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6756 (m-30) REVERT: A 25 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8047 (pt0) REVERT: A 304 GLN cc_start: 0.8473 (tt0) cc_final: 0.8265 (tt0) REVERT: A 308 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8819 (mm-30) REVERT: A 314 LYS cc_start: 0.9075 (mppt) cc_final: 0.8850 (mttp) REVERT: A 333 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7894 (tp-100) REVERT: A 351 CYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6685 (m) REVERT: S 34 MET cc_start: 0.5516 (mmp) cc_final: 0.5174 (mmm) REVERT: S 82 GLN cc_start: 0.7528 (tp40) cc_final: 0.7248 (mm-40) REVERT: S 93 MET cc_start: 0.8629 (tmm) cc_final: 0.8391 (ppp) REVERT: S 208 GLU cc_start: 0.8203 (mp0) cc_final: 0.7972 (mp0) REVERT: S 210 GLU cc_start: 0.7736 (pm20) cc_final: 0.7382 (pm20) outliers start: 33 outliers final: 26 residues processed: 182 average time/residue: 0.2334 time to fit residues: 56.2218 Evaluate side-chains 187 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 20 ASP 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 159 ASN Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 187 VAL 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 21 optimal weight: 0.0870 chunk 99 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.122570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.100636 restraints weight = 22635.448| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 4.41 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8879 Z= 0.152 Angle : 0.775 12.016 12029 Z= 0.398 Chirality : 0.045 0.187 1376 Planarity : 0.005 0.056 1498 Dihedral : 5.279 46.235 1214 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.48 % Rotamer: Outliers : 3.36 % Allowed : 20.36 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 1085 helix: 1.61 (0.26), residues: 386 sheet: -0.77 (0.29), residues: 276 loop : -1.14 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 211 HIS 0.005 0.001 HIS B 225 PHE 0.059 0.002 PHE R 182 TYR 0.030 0.002 TYR S 178 ARG 0.012 0.001 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.04526 ( 424) hydrogen bonds : angle 5.09364 ( 1185) SS BOND : bond 0.01680 ( 6) SS BOND : angle 4.01322 ( 12) covalent geometry : bond 0.00343 ( 8873) covalent geometry : angle 0.76500 (12017) ********************** 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: 32 poor density : 163 time to evaluate : 0.969 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 19 ARG cc_start: 0.8230 (mmm160) cc_final: 0.7855 (mmm160) REVERT: B 37 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.7136 (mp) REVERT: B 75 GLN cc_start: 0.8617 (mt0) cc_final: 0.8169 (mt0) REVERT: B 91 HIS cc_start: 0.7767 (m-70) cc_final: 0.7414 (m-70) REVERT: B 101 MET cc_start: 0.6645 (mpp) cc_final: 0.5864 (mmm) REVERT: B 138 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7695 (mm-30) REVERT: B 175 GLN cc_start: 0.8445 (mm110) cc_final: 0.8123 (mp10) REVERT: B 259 GLN cc_start: 0.6833 (pp30) cc_final: 0.6545 (pp30) REVERT: B 262 MET cc_start: 0.7901 (mmm) cc_final: 0.7537 (mmm) REVERT: B 325 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8010 (mmm) REVERT: G 42 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7811 (pt0) REVERT: G 44 HIS cc_start: 0.8218 (m170) cc_final: 0.7958 (t-170) REVERT: G 46 LYS cc_start: 0.9549 (tppp) cc_final: 0.9215 (tppt) REVERT: R 80 PHE cc_start: 0.6195 (OUTLIER) cc_final: 0.5820 (t80) REVERT: A 20 ASP cc_start: 0.6926 (OUTLIER) cc_final: 0.6692 (m-30) REVERT: A 25 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8131 (tm-30) REVERT: A 28 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7287 (tm-30) REVERT: A 308 GLU cc_start: 0.9293 (mm-30) cc_final: 0.8824 (mm-30) REVERT: A 314 LYS cc_start: 0.9021 (mppt) cc_final: 0.8773 (mttp) REVERT: A 333 GLN cc_start: 0.8166 (tp-100) cc_final: 0.7902 (tp40) REVERT: A 351 CYS cc_start: 0.6952 (OUTLIER) cc_final: 0.6563 (m) REVERT: S 34 MET cc_start: 0.5491 (mmp) cc_final: 0.4845 (mmm) REVERT: S 82 GLN cc_start: 0.7518 (tp40) cc_final: 0.7247 (mm-40) REVERT: S 93 MET cc_start: 0.8678 (tmm) cc_final: 0.8408 (ppp) REVERT: S 171 GLN cc_start: 0.8442 (mp10) cc_final: 0.8190 (mp10) REVERT: S 208 GLU cc_start: 0.8214 (mp0) cc_final: 0.7968 (mp0) REVERT: S 210 GLU cc_start: 0.7854 (pm20) cc_final: 0.7499 (pm20) outliers start: 32 outliers final: 25 residues processed: 180 average time/residue: 0.2534 time to fit residues: 60.3544 Evaluate side-chains 186 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 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 187 VAL 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 48 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.122226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.100338 restraints weight = 22661.857| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 4.42 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8879 Z= 0.157 Angle : 0.779 11.834 12029 Z= 0.395 Chirality : 0.045 0.186 1376 Planarity : 0.004 0.060 1498 Dihedral : 5.238 45.324 1214 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.61 % Favored : 95.30 % Rotamer: Outliers : 3.36 % Allowed : 20.78 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1085 helix: 1.59 (0.27), residues: 385 sheet: -0.79 (0.29), residues: 278 loop : -1.17 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 211 HIS 0.006 0.001 HIS B 225 PHE 0.051 0.002 PHE R 182 TYR 0.030 0.002 TYR S 178 ARG 0.010 0.001 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.04485 ( 424) hydrogen bonds : angle 5.06983 ( 1185) SS BOND : bond 0.01535 ( 6) SS BOND : angle 3.91498 ( 12) covalent geometry : bond 0.00361 ( 8873) covalent geometry : angle 0.76941 (12017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5084.96 seconds wall clock time: 88 minutes 20.48 seconds (5300.48 seconds total)