Starting phenix.real_space_refine on Sat Dec 28 13:39:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yh2_39279/12_2024/8yh2_39279.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yh2_39279/12_2024/8yh2_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_39279/12_2024/8yh2_39279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yh2_39279/12_2024/8yh2_39279.map" model { file = "/net/cci-nas-00/data/ceres_data/8yh2_39279/12_2024/8yh2_39279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yh2_39279/12_2024/8yh2_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.11, per 1000 atoms: 0.59 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: 2.32 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: 0.93 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: 2.45 Time building geometry restraints manager: 2.68 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: 0.270 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.260 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.970 ------------------------------------------------------------------------------- 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 8873 Z= 0.271 Angle : 0.629 16.040 12017 Z= 0.338 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 *********************** 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 : 1.077 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: 0.2642 time to fit residues: 94.0971 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 : 1.183 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 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 8873 Z= 0.283 Angle : 0.755 11.934 12017 Z= 0.397 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 *********************** 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 : 1.032 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: A 18 MET cc_start: 0.6700 (tpp) cc_final: 0.6292 (mmm) REVERT: A 22 ASN cc_start: 0.6658 (m110) cc_final: 0.6432 (m-40) REVERT: A 308 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8077 (mm-30) REVERT: A 333 GLN cc_start: 0.7462 (tp-100) cc_final: 0.7057 (tp-100) REVERT: A 337 ASP cc_start: 0.7302 (m-30) cc_final: 0.6569 (m-30) outliers start: 20 outliers final: 11 residues processed: 221 average time/residue: 0.2429 time to fit residues: 71.0556 Evaluate side-chains 178 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 TRP 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 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 55 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 82 optimal weight: 0.0970 chunk 67 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 30.0000 chunk 107 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8873 Z= 0.254 Angle : 0.719 12.194 12017 Z= 0.375 Chirality : 0.046 0.216 1376 Planarity : 0.004 0.044 1498 Dihedral : 5.744 57.611 1214 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.31 % Rotamer: Outliers : 2.62 % Allowed : 15.84 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1085 helix: 1.59 (0.27), residues: 370 sheet: -0.40 (0.31), residues: 264 loop : -0.99 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 184 HIS 0.014 0.001 HIS G 44 PHE 0.013 0.001 PHE A 189 TYR 0.025 0.002 TYR S 178 ARG 0.009 0.001 ARG S 148 *********************** 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 210 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 1.034 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: B 61 MET cc_start: 0.7855 (ppp) cc_final: 0.7643 (ppp) REVERT: A 18 MET cc_start: 0.6524 (tpp) cc_final: 0.6173 (mmm) REVERT: A 22 ASN cc_start: 0.6932 (m110) cc_final: 0.6549 (m-40) REVERT: A 308 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8089 (mm-30) REVERT: A 333 GLN cc_start: 0.7621 (tp-100) cc_final: 0.7238 (tp-100) REVERT: A 337 ASP cc_start: 0.7424 (m-30) cc_final: 0.6676 (m-30) outliers start: 25 outliers final: 18 residues processed: 196 average time/residue: 0.2400 time to fit residues: 62.5527 Evaluate side-chains 194 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 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 110 LEU 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 A residue 281 SER 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 97 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 0.0870 chunk 105 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 87 optimal weight: 20.0000 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 110 ASN B 220 GLN ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8873 Z= 0.254 Angle : 0.693 8.366 12017 Z= 0.363 Chirality : 0.046 0.223 1376 Planarity : 0.004 0.051 1498 Dihedral : 5.689 56.891 1214 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 2.83 % Allowed : 17.94 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1085 helix: 1.64 (0.27), residues: 370 sheet: -0.37 (0.31), residues: 259 loop : -0.98 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.009 0.002 HIS G 44 PHE 0.014 0.002 PHE R 288 TYR 0.021 0.002 TYR S 50 ARG 0.007 0.001 ARG S 148 *********************** 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 203 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7756 (m-80) cc_final: 0.7258 (m-80) REVERT: B 78 LYS cc_start: 0.7923 (tppt) cc_final: 0.7528 (tppt) REVERT: A 18 MET cc_start: 0.6495 (tpp) cc_final: 0.6196 (mmm) REVERT: A 285 ILE cc_start: 0.6232 (mp) cc_final: 0.6014 (mp) REVERT: S 145 ILE cc_start: 0.8025 (tp) cc_final: 0.7772 (tt) outliers start: 27 outliers final: 21 residues processed: 190 average time/residue: 0.2588 time to fit residues: 64.9727 Evaluate side-chains 184 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 220 GLN Chi-restraints excluded: chain B residue 308 LEU 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 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 A residue 281 SER Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 343 ILE 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 59 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 266 HIS B 295 ASN ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8873 Z= 0.276 Angle : 0.720 14.026 12017 Z= 0.372 Chirality : 0.046 0.238 1376 Planarity : 0.005 0.060 1498 Dihedral : 5.787 57.491 1214 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.58 % Rotamer: Outliers : 3.15 % Allowed : 18.99 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.26), residues: 1085 helix: 1.41 (0.27), residues: 376 sheet: -0.51 (0.30), residues: 267 loop : -1.00 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 184 HIS 0.007 0.001 HIS B 225 PHE 0.016 0.002 PHE R 288 TYR 0.029 0.002 TYR A 302 ARG 0.008 0.001 ARG S 148 *********************** 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 192 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 1.051 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 78 LYS cc_start: 0.7916 (tppt) cc_final: 0.7695 (tppt) REVERT: A 212 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8063 (tp) outliers start: 30 outliers final: 25 residues processed: 180 average time/residue: 0.2491 time to fit residues: 59.5394 Evaluate side-chains 178 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 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 149 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 308 LEU 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 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 212 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain S residue 67 ARG 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 94 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 61 optimal weight: 30.0000 chunk 26 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 55 optimal weight: 0.0470 chunk 101 optimal weight: 0.9980 overall best weight: 1.3680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8873 Z= 0.234 Angle : 0.695 11.753 12017 Z= 0.359 Chirality : 0.045 0.247 1376 Planarity : 0.004 0.060 1498 Dihedral : 5.663 56.566 1214 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 3.36 % Allowed : 19.62 % Favored : 77.02 % 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: 1.61 (0.27), residues: 375 sheet: -0.46 (0.30), residues: 261 loop : -1.05 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 184 HIS 0.006 0.001 HIS B 225 PHE 0.022 0.001 PHE S 200 TYR 0.029 0.002 TYR A 302 ARG 0.008 0.000 ARG S 148 *********************** 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 193 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 1.097 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: G 20 LYS cc_start: 0.9103 (ptpp) cc_final: 0.8791 (ptpp) REVERT: A 212 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8085 (tp) outliers start: 32 outliers final: 25 residues processed: 180 average time/residue: 0.2610 time to fit residues: 63.1257 Evaluate side-chains 176 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 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 331 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 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 212 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 287 TYR 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 11 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8873 Z= 0.215 Angle : 0.701 9.153 12017 Z= 0.361 Chirality : 0.045 0.251 1376 Planarity : 0.004 0.059 1498 Dihedral : 5.600 55.530 1214 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 2.73 % Allowed : 21.20 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1085 helix: 1.66 (0.27), residues: 377 sheet: -0.68 (0.29), residues: 274 loop : -1.04 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 184 HIS 0.006 0.001 HIS B 225 PHE 0.022 0.001 PHE S 32 TYR 0.026 0.002 TYR A 302 ARG 0.008 0.000 ARG S 148 *********************** 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 188 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.959 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 75 GLN cc_start: 0.7108 (mt0) cc_final: 0.6732 (mt0) REVERT: B 101 MET cc_start: 0.4951 (mpp) cc_final: 0.4575 (mpp) REVERT: G 20 LYS cc_start: 0.9096 (ptpp) cc_final: 0.8785 (ptpp) outliers start: 26 outliers final: 24 residues processed: 176 average time/residue: 0.2597 time to fit residues: 60.9959 Evaluate side-chains 173 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 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 331 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 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 287 TYR Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 30 ASN R 95 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8873 Z= 0.285 Angle : 0.755 10.259 12017 Z= 0.388 Chirality : 0.045 0.250 1376 Planarity : 0.005 0.055 1498 Dihedral : 5.690 55.941 1214 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.21 % Rotamer: Outliers : 3.25 % Allowed : 21.93 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (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: 1.53 (0.27), residues: 378 sheet: -0.67 (0.29), residues: 272 loop : -1.06 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 339 HIS 0.007 0.001 HIS B 225 PHE 0.017 0.002 PHE S 32 TYR 0.030 0.002 TYR S 178 ARG 0.007 0.001 ARG S 148 *********************** 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 182 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.925 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: G 20 LYS cc_start: 0.9059 (ptpp) cc_final: 0.8827 (ptpp) outliers start: 31 outliers final: 25 residues processed: 168 average time/residue: 0.2298 time to fit residues: 51.8829 Evaluate side-chains 170 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 234 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 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 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 287 TYR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 0.0000 chunk 30 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8873 Z= 0.233 Angle : 0.749 11.097 12017 Z= 0.383 Chirality : 0.046 0.260 1376 Planarity : 0.004 0.058 1498 Dihedral : 5.682 55.802 1214 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 2.94 % Allowed : 22.14 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.26), residues: 1085 helix: 1.54 (0.27), residues: 384 sheet: -0.76 (0.29), residues: 271 loop : -1.07 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP R 184 HIS 0.007 0.001 HIS B 225 PHE 0.014 0.002 PHE S 200 TYR 0.026 0.002 TYR A 302 ARG 0.009 0.000 ARG S 148 *********************** 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 179 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 1.070 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: G 20 LYS cc_start: 0.9119 (ptpp) cc_final: 0.8839 (ptpp) REVERT: A 302 TYR cc_start: 0.6034 (t80) cc_final: 0.5747 (t80) outliers start: 28 outliers final: 25 residues processed: 168 average time/residue: 0.2313 time to fit residues: 52.3263 Evaluate side-chains 169 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.4980 chunk 71 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8873 Z= 0.297 Angle : 0.807 10.660 12017 Z= 0.414 Chirality : 0.046 0.258 1376 Planarity : 0.005 0.056 1498 Dihedral : 5.864 57.992 1214 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.21 % Rotamer: Outliers : 3.04 % Allowed : 22.56 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (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: -0.24 (0.26), residues: 1085 helix: 1.41 (0.27), residues: 385 sheet: -0.72 (0.29), residues: 265 loop : -1.17 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 211 HIS 0.007 0.001 HIS B 225 PHE 0.014 0.002 PHE S 200 TYR 0.030 0.002 TYR S 178 ARG 0.010 0.001 ARG B 19 ********************** 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 177 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.988 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: G 20 LYS cc_start: 0.9118 (ptpp) cc_final: 0.8835 (ptpp) REVERT: R 90 MET cc_start: 0.3857 (mmt) cc_final: 0.3652 (mmt) outliers start: 29 outliers final: 26 residues processed: 165 average time/residue: 0.2393 time to fit residues: 53.0527 Evaluate side-chains 169 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 0.0770 chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 0.0470 chunk 4 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** A 52 GLN ** 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 = 0.4187 r_free = 0.4187 target = 0.128477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.106861 restraints weight = 22212.015| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 4.37 r_work: 0.3616 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8873 Z= 0.224 Angle : 0.808 12.732 12017 Z= 0.414 Chirality : 0.047 0.269 1376 Planarity : 0.005 0.057 1498 Dihedral : 5.704 54.126 1214 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.94 % Rotamer: Outliers : 2.62 % Allowed : 23.82 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1085 helix: 1.50 (0.27), residues: 389 sheet: -0.70 (0.30), residues: 264 loop : -1.15 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 184 HIS 0.005 0.001 HIS B 225 PHE 0.058 0.002 PHE R 182 TYR 0.029 0.002 TYR S 178 ARG 0.013 0.001 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2315.08 seconds wall clock time: 43 minutes 5.56 seconds (2585.56 seconds total)