Starting phenix.real_space_refine on Tue Apr 29 10:23:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yh2_39279/04_2025/8yh2_39279.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yh2_39279/04_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_39279/04_2025/8yh2_39279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yh2_39279/04_2025/8yh2_39279.map" model { file = "/net/cci-nas-00/data/ceres_data/8yh2_39279/04_2025/8yh2_39279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yh2_39279/04_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-5669/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: 5.26, per 1000 atoms: 0.61 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: 2.46 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: 1.08 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: 2.66 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 2790 1.36 - 1.50: 2392 1.50 - 1.63: 3593 1.63 - 1.77: 1 1.77 - 1.90: 97 Bond restraints: 8873 Sorted by residual: bond pdb=" C5 ADN R 801 " pdb=" N7 ADN R 801 " ideal model delta sigma weight residual 1.371 1.523 -0.152 2.00e-02 2.50e+03 5.80e+01 bond pdb=" C6 ADN R 801 " pdb=" N6 ADN R 801 " ideal model delta sigma weight residual 1.333 1.451 -0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" C8 ADN R 801 " pdb=" N9 ADN R 801 " ideal model delta sigma weight residual 1.370 1.255 0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C4 ADN R 801 " pdb=" C5 ADN R 801 " ideal model delta sigma weight residual 1.385 1.477 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C4 ADN R 801 " pdb=" N9 ADN R 801 " ideal model delta sigma weight residual 1.367 1.284 0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 8868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 11961 3.21 - 6.42: 45 6.42 - 9.62: 8 9.62 - 12.83: 2 12.83 - 16.04: 1 Bond angle restraints: 12017 Sorted by residual: angle pdb=" C4 ADN R 801 " pdb=" N9 ADN R 801 " pdb=" C8 ADN R 801 " ideal model delta sigma weight residual 105.99 122.03 -16.04 3.00e+00 1.11e-01 2.86e+01 angle pdb=" C CYS B 114 " pdb=" N GLY B 115 " pdb=" CA GLY B 115 " ideal model delta sigma weight residual 121.41 128.92 -7.51 1.96e+00 2.60e-01 1.47e+01 angle pdb=" CA PRO B 39 " pdb=" N PRO B 39 " pdb=" CD PRO B 39 " ideal model delta sigma weight residual 112.00 106.74 5.26 1.40e+00 5.10e-01 1.41e+01 angle pdb=" C6 ADN R 801 " pdb=" C5 ADN R 801 " pdb=" N7 ADN R 801 " ideal model delta sigma weight residual 132.88 143.60 -10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" C4 ADN R 801 " pdb=" C5 ADN R 801 " pdb=" N7 ADN R 801 " ideal model delta sigma weight residual 110.79 100.29 10.50 3.00e+00 1.11e-01 1.22e+01 ... (remaining 12012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 4686 16.11 - 32.22: 484 32.22 - 48.32: 83 48.32 - 64.43: 19 64.43 - 80.54: 8 Dihedral angle restraints: 5280 sinusoidal: 2078 harmonic: 3202 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 12.89 80.11 1 1.00e+01 1.00e-02 7.95e+01 dihedral pdb=" CA ALA B 113 " pdb=" C ALA B 113 " pdb=" N CYS B 114 " pdb=" CA CYS B 114 " ideal model delta harmonic sigma weight residual 180.00 138.11 41.89 0 5.00e+00 4.00e-02 7.02e+01 dihedral pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " pdb=" SG CYS B 114 " pdb=" CB CYS B 114 " ideal model delta sinusoidal sigma weight residual -86.00 -159.41 73.41 1 1.00e+01 1.00e-02 6.86e+01 ... (remaining 5277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1165 0.052 - 0.105: 155 0.105 - 0.157: 53 0.157 - 0.210: 1 0.210 - 0.262: 2 Chirality restraints: 1376 Sorted by residual: chirality pdb=" C3' ADN R 801 " pdb=" C2' ADN R 801 " pdb=" C4' ADN R 801 " pdb=" O3' ADN R 801 " both_signs ideal model delta sigma weight residual False -2.48 -2.74 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C2' ADN R 801 " pdb=" C1' ADN R 801 " pdb=" C3' ADN R 801 " pdb=" O2' ADN R 801 " both_signs ideal model delta sigma weight residual False -2.75 -2.50 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA CYS B 114 " pdb=" N CYS B 114 " pdb=" C CYS B 114 " pdb=" CB CYS B 114 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.14e-01 ... (remaining 1373 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " -0.051 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO B 39 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.047 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO S 75 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 113 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C ALA B 113 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA B 113 " 0.012 2.00e-02 2.50e+03 pdb=" N CYS B 114 " 0.010 2.00e-02 2.50e+03 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 91 2.57 - 3.16: 7447 3.16 - 3.74: 13233 3.74 - 4.32: 18735 4.32 - 4.90: 31575 Nonbonded interactions: 71081 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 1.993 3.040 nonbonded pdb=" OE1 GLN S 130 " pdb=" OG1 THR S 231 " model vdw 2.017 3.040 nonbonded pdb=" OE2 GLU R 19 " pdb=" ND1 HIS R 271 " model vdw 2.074 3.120 nonbonded pdb=" OG SER B 281 " pdb=" O HIS G 44 " model vdw 2.096 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.105 3.040 ... (remaining 71076 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.840 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.990 ------------------------------------------------------------------------------- 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= 0.200 Angle : 0.640 16.040 12029 Z= 0.343 Chirality : 0.042 0.262 1376 Planarity : 0.004 0.075 1498 Dihedral : 13.420 80.539 3196 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.72 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 0.00420 ( 8873) covalent geometry : angle 0.62856 (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 : 1.026 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: 0.2519 time to fit residues: 89.0519 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 : 1.116 ------------------------------------------------------------------------------- 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 = 0.127575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.105778 restraints weight = 22323.774| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 4.38 r_work: 0.3658 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 8879 Z= 0.190 Angle : 0.775 12.448 12029 Z= 0.406 Chirality : 0.048 0.231 1376 Planarity : 0.005 0.056 1498 Dihedral : 5.768 58.901 1214 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.94 % Rotamer: Outliers : 2.10 % Allowed : 11.86 % Favored : 86.04 % 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: -0.03 (0.26), residues: 1085 helix: 1.58 (0.27), residues: 375 sheet: -0.61 (0.30), residues: 268 loop : -0.97 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 184 HIS 0.004 0.001 HIS A 322 PHE 0.021 0.002 PHE R 167 TYR 0.012 0.002 TYR S 102 ARG 0.007 0.001 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.05367 ( 424) hydrogen bonds : angle 5.69866 ( 1185) SS BOND : bond 0.02446 ( 6) SS BOND : angle 5.71294 ( 12) covalent geometry : bond 0.00437 ( 8873) covalent geometry : angle 0.75454 (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 233 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 325 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8610 (mmm) REVERT: G 15 LEU cc_start: 0.9165 (tt) cc_final: 0.8955 (pp) REVERT: G 42 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7599 (pt0) REVERT: G 44 HIS cc_start: 0.8120 (m-70) cc_final: 0.7275 (t70) REVERT: R 128 TRP cc_start: 0.7614 (m100) cc_final: 0.7260 (m100) REVERT: A 18 MET cc_start: 0.8218 (tpp) cc_final: 0.7634 (mmm) REVERT: A 22 ASN cc_start: 0.7317 (m110) cc_final: 0.6847 (m-40) REVERT: A 256 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8234 (p0) REVERT: A 269 ASN cc_start: 0.6306 (p0) cc_final: 0.5830 (p0) REVERT: A 308 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8874 (mm-30) REVERT: A 333 GLN cc_start: 0.7963 (tp-100) cc_final: 0.7653 (tp-100) REVERT: A 337 ASP cc_start: 0.7590 (m-30) cc_final: 0.7093 (m-30) REVERT: A 349 LYS cc_start: 0.8125 (ttpt) cc_final: 0.7925 (ttpp) REVERT: S 82 GLN cc_start: 0.7688 (tp40) cc_final: 0.7372 (tp-100) REVERT: S 128 MET cc_start: 0.5330 (OUTLIER) cc_final: 0.4954 (mtp) REVERT: S 148 ARG cc_start: 0.7843 (mmm-85) cc_final: 0.7187 (mmm-85) REVERT: S 208 GLU cc_start: 0.8360 (mp0) cc_final: 0.8064 (mp0) outliers start: 20 outliers final: 11 residues processed: 221 average time/residue: 0.2686 time to fit residues: 78.9777 Evaluate side-chains 187 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 0.0370 chunk 27 optimal weight: 8.9990 chunk 51 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 0.0010 chunk 77 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.2868 ------------------------------------------------------------------------------- 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 ** 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 = 0.4049 r_free = 0.4049 target = 0.121489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.099498 restraints weight = 23036.164| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 4.35 r_work: 0.3625 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8879 Z= 0.162 Angle : 0.715 12.424 12029 Z= 0.373 Chirality : 0.046 0.225 1376 Planarity : 0.004 0.044 1498 Dihedral : 5.718 57.419 1214 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.31 % Rotamer: Outliers : 2.83 % Allowed : 15.53 % Favored : 81.64 % 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: 0.03 (0.26), residues: 1085 helix: 1.62 (0.27), residues: 370 sheet: -0.44 (0.30), residues: 264 loop : -1.00 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 184 HIS 0.003 0.001 HIS A 322 PHE 0.014 0.001 PHE A 189 TYR 0.026 0.002 TYR S 178 ARG 0.008 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04933 ( 424) hydrogen bonds : angle 5.33562 ( 1185) SS BOND : bond 0.01785 ( 6) SS BOND : angle 4.98524 ( 12) covalent geometry : bond 0.00366 ( 8873) covalent geometry : angle 0.69775 (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 217 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 HIS cc_start: 0.7876 (m-70) cc_final: 0.7428 (m-70) REVERT: B 175 GLN cc_start: 0.8676 (mm110) cc_final: 0.8327 (mp10) REVERT: B 264 TYR cc_start: 0.7400 (m-80) cc_final: 0.7107 (m-10) REVERT: B 325 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8549 (mmm) REVERT: B 337 LYS cc_start: 0.7854 (mttm) cc_final: 0.7578 (mttp) REVERT: G 42 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7703 (pt0) REVERT: A 18 MET cc_start: 0.8188 (tpp) cc_final: 0.7598 (mmm) REVERT: A 22 ASN cc_start: 0.7532 (m110) cc_final: 0.6959 (m-40) REVERT: A 269 ASN cc_start: 0.6321 (p0) cc_final: 0.5780 (p0) REVERT: A 287 TYR cc_start: 0.5744 (t80) cc_final: 0.5366 (t80) REVERT: A 308 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8867 (mm-30) REVERT: A 314 LYS cc_start: 0.9017 (mppt) cc_final: 0.8786 (mttm) REVERT: A 333 GLN cc_start: 0.8245 (tp-100) cc_final: 0.7815 (tp-100) REVERT: A 337 ASP cc_start: 0.7839 (m-30) cc_final: 0.7247 (m-30) REVERT: S 34 MET cc_start: 0.5387 (mmp) cc_final: 0.5032 (mmm) REVERT: S 50 TYR cc_start: 0.8328 (t80) cc_final: 0.8049 (t80) REVERT: S 82 GLN cc_start: 0.7731 (tp40) cc_final: 0.7306 (tp-100) REVERT: S 148 ARG cc_start: 0.7905 (mmm-85) cc_final: 0.7447 (mmm-85) REVERT: S 208 GLU cc_start: 0.8423 (mp0) cc_final: 0.7973 (mp0) REVERT: S 210 GLU cc_start: 0.7544 (pm20) cc_final: 0.7178 (pm20) outliers start: 27 outliers final: 17 residues processed: 200 average time/residue: 0.2540 time to fit residues: 67.8661 Evaluate side-chains 196 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR 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 83 CYS Chi-restraints excluded: chain R residue 141 VAL 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: 4.9990 chunk 27 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 3 optimal weight: 0.2980 chunk 44 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 G 44 HIS ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.117770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.095830 restraints weight = 23024.481| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 4.31 r_work: 0.3563 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 8879 Z= 0.217 Angle : 0.758 14.663 12029 Z= 0.392 Chirality : 0.047 0.223 1376 Planarity : 0.005 0.050 1498 Dihedral : 5.822 57.904 1214 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 3.15 % Allowed : 17.73 % Favored : 79.12 % 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: 1.22 (0.27), residues: 381 sheet: -0.40 (0.30), residues: 262 loop : -0.95 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.006 0.002 HIS B 225 PHE 0.014 0.002 PHE R 288 TYR 0.027 0.002 TYR S 178 ARG 0.005 0.001 ARG S 206 Details of bonding type rmsd hydrogen bonds : bond 0.05226 ( 424) hydrogen bonds : angle 5.29978 ( 1185) SS BOND : bond 0.01991 ( 6) SS BOND : angle 5.51238 ( 12) covalent geometry : bond 0.00498 ( 8873) covalent geometry : angle 0.73778 (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 201 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.963 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 91 HIS cc_start: 0.8039 (m-70) cc_final: 0.7619 (m-70) REVERT: B 175 GLN cc_start: 0.8652 (mm110) cc_final: 0.8266 (mp10) REVERT: B 262 MET cc_start: 0.7599 (mmm) cc_final: 0.7251 (mmm) REVERT: B 325 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8131 (ptp) REVERT: B 337 LYS cc_start: 0.7806 (mttm) cc_final: 0.7571 (mttp) REVERT: G 42 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7743 (pt0) REVERT: A 18 MET cc_start: 0.8296 (tpp) cc_final: 0.7991 (tpp) REVERT: A 25 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8130 (pt0) REVERT: A 314 LYS cc_start: 0.9094 (mppt) cc_final: 0.8823 (mttm) REVERT: A 318 GLU cc_start: 0.8366 (pm20) cc_final: 0.8053 (pm20) REVERT: A 333 GLN cc_start: 0.8324 (tp-100) cc_final: 0.7994 (tp-100) REVERT: S 34 MET cc_start: 0.5496 (mmp) cc_final: 0.5100 (mmm) REVERT: S 82 GLN cc_start: 0.7504 (tp40) cc_final: 0.7021 (tp-100) outliers start: 30 outliers final: 24 residues processed: 186 average time/residue: 0.2359 time to fit residues: 57.9262 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 : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 187 VAL 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 141 VAL 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 343 ILE Chi-restraints excluded: chain A residue 344 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: 1.9990 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 G 44 HIS A 22 ASN ** A 269 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.123204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.101261 restraints weight = 22718.479| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 4.42 r_work: 0.3621 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8879 Z= 0.149 Angle : 0.689 12.831 12029 Z= 0.358 Chirality : 0.045 0.242 1376 Planarity : 0.004 0.053 1498 Dihedral : 5.674 56.306 1214 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.94 % Rotamer: Outliers : 3.15 % Allowed : 19.52 % 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: 0.07 (0.26), residues: 1085 helix: 1.63 (0.27), residues: 373 sheet: -0.47 (0.30), residues: 272 loop : -0.94 (0.31), residues: 440 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 0.015 0.001 PHE R 288 TYR 0.026 0.002 TYR S 178 ARG 0.009 0.001 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.04688 ( 424) hydrogen bonds : angle 5.20466 ( 1185) SS BOND : bond 0.01889 ( 6) SS BOND : angle 4.80424 ( 12) covalent geometry : bond 0.00333 ( 8873) covalent geometry : angle 0.67239 (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 200 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 1.027 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: 0.7470 (OUTLIER) cc_final: 0.7200 (mp) REVERT: B 75 GLN cc_start: 0.8346 (tt0) cc_final: 0.8136 (tt0) REVERT: B 91 HIS cc_start: 0.8002 (m-70) cc_final: 0.7671 (m-70) REVERT: B 175 GLN cc_start: 0.8646 (mm110) cc_final: 0.8248 (mp10) REVERT: B 262 MET cc_start: 0.7586 (mmm) cc_final: 0.7160 (mmm) REVERT: B 264 TYR cc_start: 0.7468 (m-80) cc_final: 0.7200 (m-10) REVERT: B 325 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8443 (mmm) REVERT: B 337 LYS cc_start: 0.7662 (mttm) cc_final: 0.7437 (mttp) REVERT: G 42 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7788 (pt0) REVERT: G 46 LYS cc_start: 0.9540 (tppp) cc_final: 0.9116 (tppt) REVERT: A 18 MET cc_start: 0.8109 (tpp) cc_final: 0.7657 (tpp) REVERT: A 25 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8165 (pt0) REVERT: A 314 LYS cc_start: 0.9080 (mppt) cc_final: 0.8821 (mttm) REVERT: A 333 GLN cc_start: 0.8407 (tp-100) cc_final: 0.8105 (tp-100) REVERT: A 351 CYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7120 (m) REVERT: S 34 MET cc_start: 0.5449 (mmp) cc_final: 0.5040 (mmm) REVERT: S 82 GLN cc_start: 0.7665 (tp40) cc_final: 0.7153 (tp40) REVERT: S 93 MET cc_start: 0.8667 (tmm) cc_final: 0.8390 (ppp) REVERT: S 174 GLN cc_start: 0.8174 (tt0) cc_final: 0.7713 (mm-40) outliers start: 30 outliers final: 22 residues processed: 189 average time/residue: 0.2500 time to fit residues: 62.4678 Evaluate side-chains 182 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 65 THR 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 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 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 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: 0.9980 chunk 95 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 29 optimal weight: 0.0770 chunk 106 optimal weight: 10.0000 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN 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 = 0.4134 r_free = 0.4134 target = 0.125423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.103587 restraints weight = 22370.936| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 4.30 r_work: 0.3642 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8879 Z= 0.144 Angle : 0.696 12.259 12029 Z= 0.360 Chirality : 0.045 0.241 1376 Planarity : 0.004 0.056 1498 Dihedral : 5.568 56.225 1214 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.61 % Favored : 95.30 % Rotamer: Outliers : 3.25 % Allowed : 19.52 % Favored : 77.23 % 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: 1.68 (0.27), residues: 375 sheet: -0.48 (0.31), residues: 256 loop : -0.98 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 184 HIS 0.005 0.001 HIS B 225 PHE 0.022 0.002 PHE S 200 TYR 0.027 0.002 TYR S 178 ARG 0.004 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04512 ( 424) hydrogen bonds : angle 5.09174 ( 1185) SS BOND : bond 0.01790 ( 6) SS BOND : angle 4.57467 ( 12) covalent geometry : bond 0.00321 ( 8873) covalent geometry : angle 0.68074 (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 188 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.7230 (mp) REVERT: B 91 HIS cc_start: 0.7860 (m-70) cc_final: 0.7533 (m-70) REVERT: B 175 GLN cc_start: 0.8658 (mm110) cc_final: 0.8280 (mp10) REVERT: B 258 ASP cc_start: 0.6861 (m-30) cc_final: 0.6656 (t70) REVERT: B 262 MET cc_start: 0.7540 (mmm) cc_final: 0.7187 (mmm) REVERT: B 325 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8388 (mmm) REVERT: G 42 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7866 (pt0) REVERT: G 46 LYS cc_start: 0.9543 (tppp) cc_final: 0.9152 (tppt) REVERT: A 25 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8166 (pt0) REVERT: A 314 LYS cc_start: 0.9086 (mppt) cc_final: 0.8779 (mttm) REVERT: A 333 GLN cc_start: 0.8376 (tp-100) cc_final: 0.8069 (tp-100) REVERT: A 351 CYS cc_start: 0.7395 (OUTLIER) cc_final: 0.6999 (m) REVERT: S 34 MET cc_start: 0.5574 (mmp) cc_final: 0.5164 (mmm) REVERT: S 82 GLN cc_start: 0.7754 (tp40) cc_final: 0.7326 (tp40) REVERT: S 93 MET cc_start: 0.8581 (tmm) cc_final: 0.8299 (ppp) REVERT: S 174 GLN cc_start: 0.8214 (tt0) cc_final: 0.7761 (mm-40) REVERT: S 208 GLU cc_start: 0.8139 (mp0) cc_final: 0.7908 (mp0) outliers start: 31 outliers final: 26 residues processed: 176 average time/residue: 0.2414 time to fit residues: 56.4855 Evaluate side-chains 175 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 65 THR 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 17 GLU 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 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 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: 3.9990 chunk 18 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN G 44 HIS R 95 HIS ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.119815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.097893 restraints weight = 22871.879| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 4.31 r_work: 0.3611 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8879 Z= 0.170 Angle : 0.733 16.912 12029 Z= 0.373 Chirality : 0.045 0.252 1376 Planarity : 0.004 0.056 1498 Dihedral : 5.571 55.885 1214 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.48 % Rotamer: Outliers : 3.67 % Allowed : 20.46 % 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: 0.08 (0.26), residues: 1085 helix: 1.66 (0.27), residues: 378 sheet: -0.55 (0.30), residues: 274 loop : -0.92 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 184 HIS 0.006 0.001 HIS B 225 PHE 0.018 0.002 PHE S 200 TYR 0.027 0.002 TYR S 178 ARG 0.008 0.000 ARG S 206 Details of bonding type rmsd hydrogen bonds : bond 0.04672 ( 424) hydrogen bonds : angle 5.12067 ( 1185) SS BOND : bond 0.01882 ( 6) SS BOND : angle 4.83424 ( 12) covalent geometry : bond 0.00390 ( 8873) covalent geometry : angle 0.71761 (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 194 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.958 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: 0.7422 (OUTLIER) cc_final: 0.7141 (mp) REVERT: B 91 HIS cc_start: 0.7984 (m-70) cc_final: 0.7577 (m-70) REVERT: B 175 GLN cc_start: 0.8668 (mm110) cc_final: 0.8288 (mp10) REVERT: B 217 MET cc_start: 0.8648 (ptt) cc_final: 0.8401 (ptt) REVERT: B 325 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8425 (mmm) REVERT: G 42 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7911 (pt0) REVERT: G 46 LYS cc_start: 0.9520 (tppp) cc_final: 0.9126 (tppt) REVERT: A 25 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8199 (pt0) REVERT: A 214 CYS cc_start: 0.9226 (m) cc_final: 0.8841 (t) REVERT: A 302 TYR cc_start: 0.8498 (t80) cc_final: 0.7813 (t80) REVERT: A 314 LYS cc_start: 0.9108 (mppt) cc_final: 0.8793 (mttm) REVERT: A 333 GLN cc_start: 0.8381 (tp-100) cc_final: 0.8093 (tp-100) REVERT: A 351 CYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7141 (m) REVERT: S 34 MET cc_start: 0.5711 (mmp) cc_final: 0.5350 (mmm) REVERT: S 82 GLN cc_start: 0.7775 (tp40) cc_final: 0.7503 (mm-40) REVERT: S 93 MET cc_start: 0.8598 (tmm) cc_final: 0.8291 (ppp) REVERT: S 208 GLU cc_start: 0.8164 (mp0) cc_final: 0.7938 (mp0) outliers start: 35 outliers final: 30 residues processed: 180 average time/residue: 0.2432 time to fit residues: 58.0724 Evaluate side-chains 186 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 65 THR 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 17 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 64 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 173 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 A residue 343 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 101 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 75 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS ** 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 = 0.4173 r_free = 0.4173 target = 0.127489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.105615 restraints weight = 22652.452| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 4.43 r_work: 0.3585 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8879 Z= 0.144 Angle : 0.738 11.839 12029 Z= 0.381 Chirality : 0.045 0.264 1376 Planarity : 0.004 0.053 1498 Dihedral : 5.514 54.832 1214 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.58 % Rotamer: Outliers : 3.57 % Allowed : 21.41 % Favored : 75.03 % 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: 1.82 (0.27), residues: 378 sheet: -0.56 (0.31), residues: 263 loop : -1.02 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP R 184 HIS 0.006 0.001 HIS B 225 PHE 0.017 0.001 PHE S 200 TYR 0.028 0.002 TYR S 178 ARG 0.011 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 424) hydrogen bonds : angle 5.11701 ( 1185) SS BOND : bond 0.01752 ( 6) SS BOND : angle 4.39469 ( 12) covalent geometry : bond 0.00320 ( 8873) covalent geometry : angle 0.72519 (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 194 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 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: 0.7445 (OUTLIER) cc_final: 0.7186 (mp) REVERT: B 75 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8285 (mt0) REVERT: B 91 HIS cc_start: 0.7815 (m-70) cc_final: 0.7410 (m-70) REVERT: B 138 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7891 (mm-30) REVERT: B 175 GLN cc_start: 0.8745 (mm110) cc_final: 0.8392 (mp10) REVERT: B 262 MET cc_start: 0.7772 (mmm) cc_final: 0.7483 (mmm) REVERT: B 325 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8300 (mmm) REVERT: G 42 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7793 (pt0) REVERT: G 46 LYS cc_start: 0.9512 (tppp) cc_final: 0.9116 (tppt) REVERT: A 25 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8234 (pt0) REVERT: A 214 CYS cc_start: 0.9198 (m) cc_final: 0.8819 (t) REVERT: A 314 LYS cc_start: 0.9093 (mppt) cc_final: 0.8873 (mttp) REVERT: A 333 GLN cc_start: 0.8366 (tp-100) cc_final: 0.8088 (tp-100) REVERT: A 351 CYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6910 (m) REVERT: S 34 MET cc_start: 0.5635 (mmp) cc_final: 0.5271 (mmm) REVERT: S 82 GLN cc_start: 0.7754 (tp40) cc_final: 0.7491 (mm-40) REVERT: S 93 MET cc_start: 0.8687 (tmm) cc_final: 0.8435 (ppp) REVERT: S 174 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7762 (mm-40) REVERT: S 210 GLU cc_start: 0.7553 (pm20) cc_final: 0.7325 (pm20) outliers start: 34 outliers final: 27 residues processed: 180 average time/residue: 0.2406 time to fit residues: 57.4877 Evaluate side-chains 184 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN 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 17 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 173 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 A residue 351 CYS Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 4 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4067 r_free = 0.4067 target = 0.120750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.098890 restraints weight = 22739.008| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 4.36 r_work: 0.3594 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8879 Z= 0.174 Angle : 0.755 12.563 12029 Z= 0.389 Chirality : 0.045 0.261 1376 Planarity : 0.005 0.057 1498 Dihedral : 5.643 55.930 1214 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.21 % Rotamer: Outliers : 3.46 % Allowed : 21.09 % Favored : 75.45 % 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: 1.73 (0.27), residues: 374 sheet: -0.66 (0.30), residues: 273 loop : -1.05 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 211 HIS 0.006 0.001 HIS B 225 PHE 0.015 0.002 PHE S 200 TYR 0.031 0.002 TYR S 178 ARG 0.013 0.001 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04683 ( 424) hydrogen bonds : angle 5.17100 ( 1185) SS BOND : bond 0.01840 ( 6) SS BOND : angle 4.61146 ( 12) covalent geometry : bond 0.00401 ( 8873) covalent geometry : angle 0.74108 (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 189 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.7213 (mp) REVERT: B 75 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8404 (mt0) REVERT: B 91 HIS cc_start: 0.7957 (m-70) cc_final: 0.7517 (m-70) REVERT: B 175 GLN cc_start: 0.8771 (mm110) cc_final: 0.8395 (mp10) REVERT: B 259 GLN cc_start: 0.6466 (pp30) cc_final: 0.6238 (pp30) REVERT: B 262 MET cc_start: 0.7824 (mmm) cc_final: 0.7507 (mmm) REVERT: B 325 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8469 (mmm) REVERT: G 42 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7778 (pt0) REVERT: G 46 LYS cc_start: 0.9550 (tppp) cc_final: 0.9126 (tppt) REVERT: A 25 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8082 (pt0) REVERT: A 214 CYS cc_start: 0.9235 (m) cc_final: 0.8869 (t) REVERT: A 302 TYR cc_start: 0.8473 (t80) cc_final: 0.7671 (t80) REVERT: A 308 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8828 (mm-30) REVERT: A 314 LYS cc_start: 0.9100 (mppt) cc_final: 0.8842 (mttp) REVERT: A 333 GLN cc_start: 0.8348 (tp-100) cc_final: 0.8109 (tp40) REVERT: A 351 CYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6618 (m) REVERT: S 34 MET cc_start: 0.5557 (mmp) cc_final: 0.5216 (mmm) REVERT: S 82 GLN cc_start: 0.7805 (tp40) cc_final: 0.7514 (mm-40) REVERT: S 93 MET cc_start: 0.8727 (tmm) cc_final: 0.8495 (ppp) REVERT: S 171 GLN cc_start: 0.8670 (mp10) cc_final: 0.8369 (mp10) REVERT: S 208 GLU cc_start: 0.8358 (mp0) cc_final: 0.7903 (mp0) REVERT: S 210 GLU cc_start: 0.7329 (pm20) cc_final: 0.7024 (pm20) outliers start: 33 outliers final: 27 residues processed: 175 average time/residue: 0.2295 time to fit residues: 53.9987 Evaluate side-chains 181 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 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 17 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 173 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 A residue 351 CYS Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 21 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS R 30 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.124404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.102849 restraints weight = 22694.555| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 4.38 r_work: 0.3581 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8879 Z= 0.181 Angle : 0.767 12.843 12029 Z= 0.398 Chirality : 0.046 0.264 1376 Planarity : 0.005 0.055 1498 Dihedral : 5.800 58.456 1214 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.39 % Rotamer: Outliers : 3.46 % Allowed : 21.20 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (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: 1.66 (0.27), residues: 374 sheet: -0.73 (0.29), residues: 273 loop : -1.10 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 211 HIS 0.007 0.001 HIS B 225 PHE 0.064 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 0.04809 ( 424) hydrogen bonds : angle 5.22729 ( 1185) SS BOND : bond 0.01901 ( 6) SS BOND : angle 4.72870 ( 12) covalent geometry : bond 0.00415 ( 8873) covalent geometry : angle 0.75287 (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 182 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7207 (mp) REVERT: B 75 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8495 (mt0) REVERT: B 91 HIS cc_start: 0.8032 (m-70) cc_final: 0.7567 (m-70) REVERT: B 101 MET cc_start: 0.6733 (mpp) cc_final: 0.5797 (mmm) REVERT: B 175 GLN cc_start: 0.8756 (mm110) cc_final: 0.8386 (mp10) REVERT: B 262 MET cc_start: 0.7882 (mmm) cc_final: 0.7551 (mmm) REVERT: B 325 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8520 (mmm) REVERT: G 42 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7880 (pt0) REVERT: G 46 LYS cc_start: 0.9553 (tppp) cc_final: 0.9127 (tppt) REVERT: R 80 PHE cc_start: 0.6740 (OUTLIER) cc_final: 0.5949 (t80) REVERT: A 25 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8031 (pt0) REVERT: A 28 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7366 (tm-30) REVERT: A 214 CYS cc_start: 0.9241 (m) cc_final: 0.8923 (t) REVERT: A 314 LYS cc_start: 0.9057 (mppt) cc_final: 0.8752 (mttm) REVERT: A 333 GLN cc_start: 0.8390 (tp-100) cc_final: 0.8155 (tp40) REVERT: A 351 CYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6715 (m) REVERT: S 34 MET cc_start: 0.5594 (mmp) cc_final: 0.5235 (mmm) REVERT: S 82 GLN cc_start: 0.7729 (tp40) cc_final: 0.7451 (mm-40) REVERT: S 93 MET cc_start: 0.8728 (tmm) cc_final: 0.8490 (ppp) REVERT: S 171 GLN cc_start: 0.8635 (mp10) cc_final: 0.8361 (mp10) REVERT: S 208 GLU cc_start: 0.8356 (mp0) cc_final: 0.7892 (mp0) REVERT: S 210 GLU cc_start: 0.7245 (pm20) cc_final: 0.6996 (pm20) outliers start: 33 outliers final: 27 residues processed: 169 average time/residue: 0.2223 time to fit residues: 50.7288 Evaluate side-chains 180 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 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 17 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 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 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: 0.7980 chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 79 optimal weight: 0.0770 chunk 68 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 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 = 0.4066 r_free = 0.4066 target = 0.120506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.098533 restraints weight = 22767.024| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 4.44 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8879 Z= 0.166 Angle : 0.755 12.074 12029 Z= 0.389 Chirality : 0.046 0.274 1376 Planarity : 0.004 0.056 1498 Dihedral : 5.684 56.664 1214 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 3.57 % Allowed : 21.20 % Favored : 75.24 % 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: -0.05 (0.26), residues: 1085 helix: 1.71 (0.27), residues: 378 sheet: -0.75 (0.29), residues: 273 loop : -1.06 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 211 HIS 0.007 0.001 HIS B 225 PHE 0.052 0.002 PHE R 182 TYR 0.020 0.002 TYR S 103 ARG 0.011 0.001 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.04673 ( 424) hydrogen bonds : angle 5.14169 ( 1185) SS BOND : bond 0.01781 ( 6) SS BOND : angle 4.49024 ( 12) covalent geometry : bond 0.00382 ( 8873) covalent geometry : angle 0.74198 (12017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5642.95 seconds wall clock time: 98 minutes 23.43 seconds (5903.43 seconds total)