Starting phenix.real_space_refine on Thu Jul 2 01:01:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r3e_53555/07_2026/9r3e_53555.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r3e_53555/07_2026/9r3e_53555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r3e_53555/07_2026/9r3e_53555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r3e_53555/07_2026/9r3e_53555.map" model { file = "/net/cci-nas-00/data/ceres_data/9r3e_53555/07_2026/9r3e_53555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r3e_53555/07_2026/9r3e_53555.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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 18 5.16 5 C 3062 2.51 5 N 810 2.21 5 O 902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4792 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2396 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 8, 'TRANS': 289} Chain: "C" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2396 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 8, 'TRANS': 289} Time building chain proxies: 1.28, per 1000 atoms: 0.27 Number of scatterers: 4792 At special positions: 0 Unit cell: (64.603, 62.086, 119.977, 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 18 16.00 O 902 8.00 N 810 7.00 C 3062 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 128.1 milliseconds 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1132 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 60.9% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'B' and resid 32 through 38 removed outlier: 4.613A pdb=" N THR B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 55 removed outlier: 3.661A pdb=" N SER B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 64 removed outlier: 3.786A pdb=" N LYS B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER B 64 " --> pdb=" O PRO B 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 59 through 64' Processing helix chain 'B' and resid 64 through 80 removed outlier: 3.739A pdb=" N ILE B 69 " --> pdb=" O TRP B 65 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 70 " --> pdb=" O LYS B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 96 removed outlier: 3.788A pdb=" N LEU B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS B 95 " --> pdb=" O GLN B 91 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU B 96 " --> pdb=" O LYS B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 111 Processing helix chain 'B' and resid 123 through 131 removed outlier: 4.703A pdb=" N GLU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 139 through 156 removed outlier: 4.679A pdb=" N LEU B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 removed outlier: 3.744A pdb=" N GLN B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 195 removed outlier: 4.315A pdb=" N GLN B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 removed outlier: 3.955A pdb=" N ILE B 215 " --> pdb=" O PRO B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.791A pdb=" N ASN B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 220 through 225' Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.726A pdb=" N TYR B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 262 removed outlier: 4.344A pdb=" N GLN B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 297 Processing helix chain 'B' and resid 309 through 325 Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.634A pdb=" N SER C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 removed outlier: 3.830A pdb=" N LYS C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER C 64 " --> pdb=" O PRO C 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 59 through 64' Processing helix chain 'C' and resid 64 through 79 removed outlier: 3.609A pdb=" N ILE C 69 " --> pdb=" O TRP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 96 removed outlier: 3.654A pdb=" N LEU C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS C 95 " --> pdb=" O GLN C 91 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU C 96 " --> pdb=" O LYS C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 111 Processing helix chain 'C' and resid 123 through 131 removed outlier: 4.668A pdb=" N GLU C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 139 through 156 removed outlier: 4.660A pdb=" N LEU C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 176 removed outlier: 3.753A pdb=" N GLN C 175 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 194 Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.829A pdb=" N ILE C 215 " --> pdb=" O PRO C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.703A pdb=" N ASN C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 225' Processing helix chain 'C' and resid 228 through 234 removed outlier: 3.562A pdb=" N MET C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 241 removed outlier: 3.738A pdb=" N TYR C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 254 Processing helix chain 'C' and resid 255 through 263 removed outlier: 4.108A pdb=" N GLN C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 297 Processing helix chain 'C' and resid 309 through 325 Processing sheet with id=AA1, first strand: chain 'B' and resid 181 through 182 removed outlier: 6.724A pdb=" N LEU B 182 " --> pdb=" O HIS B 204 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 203 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 43 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N LEU B 160 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 45 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 44 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU B 247 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL B 46 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N PHE B 244 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU B 277 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE B 246 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 181 through 182 removed outlier: 6.722A pdb=" N LEU C 182 " --> pdb=" O HIS C 204 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 203 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU C 43 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU C 160 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU C 45 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL C 44 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU C 247 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 46 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE C 244 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU C 277 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE C 246 " --> pdb=" O LEU C 277 " (cutoff:3.500A) 188 hydrogen bonds defined for protein. 540 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: 0.65 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 827 1.27 - 1.41: 1124 1.41 - 1.54: 2836 1.54 - 1.68: 65 1.68 - 1.81: 28 Bond restraints: 4880 Sorted by residual: bond pdb=" CG PHE C 90 " pdb=" CD2 PHE C 90 " ideal model delta sigma weight residual 1.384 1.252 0.132 2.10e-02 2.27e+03 3.94e+01 bond pdb=" CG ASN C 166 " pdb=" ND2 ASN C 166 " ideal model delta sigma weight residual 1.328 1.212 0.116 2.10e-02 2.27e+03 3.04e+01 bond pdb=" CG ASN C 166 " pdb=" OD1 ASN C 166 " ideal model delta sigma weight residual 1.231 1.140 0.091 1.90e-02 2.77e+03 2.29e+01 bond pdb=" CB PHE C 90 " pdb=" CG PHE C 90 " ideal model delta sigma weight residual 1.502 1.394 0.108 2.30e-02 1.89e+03 2.20e+01 bond pdb=" CB ASN C 166 " pdb=" CG ASN C 166 " ideal model delta sigma weight residual 1.516 1.400 0.116 2.50e-02 1.60e+03 2.15e+01 ... (remaining 4875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.61: 6440 4.61 - 9.22: 118 9.22 - 13.84: 18 13.84 - 18.45: 2 18.45 - 23.06: 2 Bond angle restraints: 6580 Sorted by residual: angle pdb=" CB LYS C 110 " pdb=" CG LYS C 110 " pdb=" CD LYS C 110 " ideal model delta sigma weight residual 111.30 92.79 18.51 2.30e+00 1.89e-01 6.48e+01 angle pdb=" CD LYS B 110 " pdb=" CE LYS B 110 " pdb=" NZ LYS B 110 " ideal model delta sigma weight residual 111.90 88.84 23.06 3.20e+00 9.77e-02 5.19e+01 angle pdb=" C HIS C 274 " pdb=" N PHE C 275 " pdb=" CA PHE C 275 " ideal model delta sigma weight residual 122.36 111.32 11.04 1.60e+00 3.91e-01 4.76e+01 angle pdb=" CD LYS C 299 " pdb=" CE LYS C 299 " pdb=" NZ LYS C 299 " ideal model delta sigma weight residual 111.90 129.75 -17.85 3.20e+00 9.77e-02 3.11e+01 angle pdb=" N ARG B 324 " pdb=" CA ARG B 324 " pdb=" C ARG B 324 " ideal model delta sigma weight residual 113.28 106.67 6.61 1.22e+00 6.72e-01 2.93e+01 ... (remaining 6575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 2673 16.82 - 33.64: 253 33.64 - 50.46: 41 50.46 - 67.27: 7 67.27 - 84.09: 6 Dihedral angle restraints: 2980 sinusoidal: 1238 harmonic: 1742 Sorted by residual: dihedral pdb=" CA ARG C 119 " pdb=" C ARG C 119 " pdb=" N SER C 120 " pdb=" CA SER C 120 " ideal model delta harmonic sigma weight residual -180.00 -154.38 -25.62 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA MET B 293 " pdb=" C MET B 293 " pdb=" N LEU B 294 " pdb=" CA LEU B 294 " ideal model delta harmonic sigma weight residual 180.00 154.52 25.48 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA MET C 293 " pdb=" C MET C 293 " pdb=" N LEU C 294 " pdb=" CA LEU C 294 " ideal model delta harmonic sigma weight residual 180.00 155.07 24.93 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 2977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 708 0.166 - 0.333: 36 0.333 - 0.499: 2 0.499 - 0.665: 1 0.665 - 0.831: 1 Chirality restraints: 748 Sorted by residual: chirality pdb=" CG LEU C 200 " pdb=" CB LEU C 200 " pdb=" CD1 LEU C 200 " pdb=" CD2 LEU C 200 " both_signs ideal model delta sigma weight residual False -2.59 -1.76 -0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" CB ILE B 215 " pdb=" CA ILE B 215 " pdb=" CG1 ILE B 215 " pdb=" CG2 ILE B 215 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.31e+00 chirality pdb=" CB ILE C 321 " pdb=" CA ILE C 321 " pdb=" CG1 ILE C 321 " pdb=" CG2 ILE C 321 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.74e+00 ... (remaining 745 not shown) Planarity restraints: 836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 275 " 0.034 2.00e-02 2.50e+03 5.95e-02 6.19e+01 pdb=" CG PHE C 275 " -0.122 2.00e-02 2.50e+03 pdb=" CD1 PHE C 275 " 0.081 2.00e-02 2.50e+03 pdb=" CD2 PHE C 275 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE C 275 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 PHE C 275 " 0.034 2.00e-02 2.50e+03 pdb=" CZ PHE C 275 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 90 " 0.061 2.00e-02 2.50e+03 5.71e-02 5.71e+01 pdb=" CG PHE B 90 " -0.132 2.00e-02 2.50e+03 pdb=" CD1 PHE B 90 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE B 90 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 90 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 90 " 0.024 2.00e-02 2.50e+03 pdb=" CZ PHE B 90 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 169 " -0.027 2.00e-02 2.50e+03 6.72e-02 4.52e+01 pdb=" CD GLU C 169 " 0.116 2.00e-02 2.50e+03 pdb=" OE1 GLU C 169 " -0.045 2.00e-02 2.50e+03 pdb=" OE2 GLU C 169 " -0.044 2.00e-02 2.50e+03 ... (remaining 833 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 277 2.71 - 3.26: 5491 3.26 - 3.80: 7839 3.80 - 4.35: 10113 4.35 - 4.90: 15348 Nonbonded interactions: 39068 Sorted by model distance: nonbonded pdb=" O ARG B 316 " pdb=" OE1 GLU B 320 " model vdw 2.160 3.040 nonbonded pdb=" O ARG C 316 " pdb=" OE1 GLU C 320 " model vdw 2.230 3.040 nonbonded pdb=" O ARG B 324 " pdb=" NE ARG B 324 " model vdw 2.262 3.120 nonbonded pdb=" N GLU C 83 " pdb=" OE2 GLU C 86 " model vdw 2.303 3.120 nonbonded pdb=" O LYS B 66 " pdb=" OE1 GLN B 70 " model vdw 2.330 3.040 ... (remaining 39063 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'C' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 8.820 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 5.660 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3687 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 : 0.012 0.139 4880 Z= 0.485 Angle : 1.556 23.061 6580 Z= 0.779 Chirality : 0.085 0.831 748 Planarity : 0.014 0.120 836 Dihedral : 13.653 84.093 1848 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 47.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.28 % Favored : 91.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.32), residues: 592 helix: -1.84 (0.27), residues: 292 sheet: -2.80 (0.70), residues: 48 loop : -1.73 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.004 ARG B 41 TYR 0.032 0.005 TYR C 222 PHE 0.132 0.008 PHE B 90 TRP 0.022 0.005 TRP B 193 HIS 0.071 0.011 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.01171 / 0.48 ( 4880) covalent geometry : angle 1.55574 / 0.78 ( 6580) hydrogen bonds : bond 0.15930 / 10.54 ( 188) hydrogen bonds : angle 7.35792 / 5.13 ( 540) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.071 Fit side-chains REVERT: B 96 GLU cc_start: 0.4381 (mp0) cc_final: 0.4097 (mp0) REVERT: B 110 LYS cc_start: 0.7117 (pttt) cc_final: 0.6468 (tptt) REVERT: B 138 MET cc_start: 0.1604 (tpt) cc_final: -0.1863 (mtt) REVERT: B 154 GLU cc_start: 0.8839 (pt0) cc_final: 0.8165 (pp20) REVERT: B 237 LYS cc_start: 0.7271 (ptpt) cc_final: 0.6719 (mmtm) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0663 time to fit residues: 2.7869 Evaluate side-chains 18 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.0030 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.0000 chunk 2 optimal weight: 0.0570 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.0070 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 0.0470 overall best weight: 0.0228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.079081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.075159 restraints weight = 15802.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.076059 restraints weight = 11372.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.076822 restraints weight = 8440.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.077319 restraints weight = 6315.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.077658 restraints weight = 4771.981| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2990 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4880 Z= 0.158 Angle : 0.797 8.867 6580 Z= 0.414 Chirality : 0.049 0.173 748 Planarity : 0.006 0.046 836 Dihedral : 5.595 18.125 634 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.37 % Allowed : 6.74 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.34), residues: 592 helix: -0.86 (0.29), residues: 286 sheet: -2.51 (0.54), residues: 70 loop : -1.45 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 233 TYR 0.014 0.002 TYR B 128 PHE 0.024 0.002 PHE C 314 TRP 0.007 0.001 TRP B 65 HIS 0.008 0.003 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 ( 4880) covalent geometry : angle 0.79664 / 0.41 ( 6580) hydrogen bonds : bond 0.04324 / 2.90 ( 188) hydrogen bonds : angle 5.27582 / 3.73 ( 540) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: C 209 TYR cc_start: 0.4694 (p90) cc_final: 0.4292 (p90) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.0696 time to fit residues: 3.8002 Evaluate side-chains 19 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 0.0980 chunk 49 optimal weight: 0.0470 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 0.1980 chunk 28 optimal weight: 6.9990 chunk 46 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.3980 chunk 25 optimal weight: 0.1980 chunk 48 optimal weight: 0.0050 overall best weight: 0.1092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.091136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.088003 restraints weight = 10742.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.088907 restraints weight = 7264.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.089562 restraints weight = 5026.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.090016 restraints weight = 3532.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.090274 restraints weight = 2462.038| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2747 moved from start: 0.6599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4880 Z= 0.139 Angle : 0.730 8.417 6580 Z= 0.379 Chirality : 0.047 0.145 748 Planarity : 0.004 0.040 836 Dihedral : 5.237 15.846 634 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.34), residues: 592 helix: -0.47 (0.30), residues: 294 sheet: -2.80 (0.57), residues: 60 loop : -1.32 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 41 TYR 0.011 0.002 TYR C 313 PHE 0.017 0.002 PHE B 314 TRP 0.006 0.001 TRP C 193 HIS 0.004 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 4880) covalent geometry : angle 0.73006 / 0.38 ( 6580) hydrogen bonds : bond 0.03968 / 2.66 ( 188) hydrogen bonds : angle 4.96081 / 3.52 ( 540) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: B 96 GLU cc_start: 0.4433 (mp0) cc_final: 0.3493 (mp0) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1022 time to fit residues: 3.8224 Evaluate side-chains 17 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 38 optimal weight: 0.0060 chunk 47 optimal weight: 3.9990 chunk 14 optimal weight: 0.1980 chunk 36 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.0030 chunk 28 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 overall best weight: 0.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 58 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.092522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.089783 restraints weight = 10868.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.090564 restraints weight = 7546.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.091148 restraints weight = 5262.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.091455 restraints weight = 3657.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.091771 restraints weight = 2725.040| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2698 moved from start: 0.7079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4880 Z= 0.130 Angle : 0.727 10.306 6580 Z= 0.369 Chirality : 0.047 0.217 748 Planarity : 0.004 0.033 836 Dihedral : 5.033 14.742 634 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.37 % Allowed : 4.87 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.34), residues: 592 helix: -0.31 (0.29), residues: 296 sheet: -2.76 (0.58), residues: 56 loop : -1.31 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 233 TYR 0.012 0.002 TYR C 313 PHE 0.016 0.001 PHE C 90 TRP 0.004 0.001 TRP B 251 HIS 0.007 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 4880) covalent geometry : angle 0.72663 / 0.37 ( 6580) hydrogen bonds : bond 0.03604 / 2.44 ( 188) hydrogen bonds : angle 4.92248 / 3.51 ( 540) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.079 Fit side-chains revert: symmetry clash REVERT: B 110 LYS cc_start: 0.6473 (pttt) cc_final: 0.5905 (tptt) REVERT: B 153 MET cc_start: 0.7291 (mmp) cc_final: 0.6918 (mmp) outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.1088 time to fit residues: 2.6253 Evaluate side-chains 12 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 32 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 56 optimal weight: 0.0670 chunk 31 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 0.0370 chunk 53 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 48 optimal weight: 0.0570 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.093566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.091180 restraints weight = 10819.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.091803 restraints weight = 7616.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.092288 restraints weight = 5495.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.092629 restraints weight = 3952.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.092874 restraints weight = 2831.667| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2701 moved from start: 0.7507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4880 Z= 0.137 Angle : 0.727 8.315 6580 Z= 0.373 Chirality : 0.046 0.186 748 Planarity : 0.004 0.027 836 Dihedral : 4.972 17.014 634 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.33), residues: 592 helix: -0.35 (0.29), residues: 294 sheet: -2.72 (0.61), residues: 56 loop : -1.32 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 233 TYR 0.009 0.002 TYR C 313 PHE 0.009 0.001 PHE C 90 TRP 0.003 0.001 TRP C 193 HIS 0.006 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 4880) covalent geometry : angle 0.72739 / 0.37 ( 6580) hydrogen bonds : bond 0.03746 / 2.49 ( 188) hydrogen bonds : angle 5.01050 / 3.60 ( 540) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: B 110 LYS cc_start: 0.6349 (pttt) cc_final: 0.6025 (tptt) REVERT: B 138 MET cc_start: 0.0841 (tpt) cc_final: -0.3034 (mtt) REVERT: B 153 MET cc_start: 0.7113 (mmp) cc_final: 0.6770 (mmp) REVERT: B 210 THR cc_start: 0.6886 (p) cc_final: 0.6299 (t) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1069 time to fit residues: 2.3653 Evaluate side-chains 13 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 38 optimal weight: 0.0050 chunk 14 optimal weight: 4.9990 chunk 46 optimal weight: 0.2980 chunk 47 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 32 optimal weight: 0.0370 chunk 15 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.0030 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 0.0980 overall best weight: 0.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.093779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.090758 restraints weight = 10495.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.091513 restraints weight = 7464.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.092113 restraints weight = 5429.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.092538 restraints weight = 3961.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.092839 restraints weight = 2906.003| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2741 moved from start: 0.7740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4880 Z= 0.136 Angle : 0.729 10.758 6580 Z= 0.370 Chirality : 0.046 0.150 748 Planarity : 0.004 0.026 836 Dihedral : 4.992 18.521 634 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.33), residues: 592 helix: -0.37 (0.29), residues: 292 sheet: -2.58 (0.62), residues: 56 loop : -1.36 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 233 TYR 0.011 0.001 TYR C 313 PHE 0.013 0.001 PHE B 90 TRP 0.003 0.001 TRP B 251 HIS 0.004 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 4880) covalent geometry : angle 0.72893 / 0.37 ( 6580) hydrogen bonds : bond 0.03716 / 2.48 ( 188) hydrogen bonds : angle 4.99121 / 3.57 ( 540) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: B 110 LYS cc_start: 0.6386 (pttt) cc_final: 0.6165 (tptt) REVERT: B 138 MET cc_start: 0.0605 (tpt) cc_final: -0.3047 (mtt) REVERT: B 153 MET cc_start: 0.7112 (mmp) cc_final: 0.6584 (mmp) REVERT: B 210 THR cc_start: 0.7104 (p) cc_final: 0.6583 (t) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0758 time to fit residues: 1.5261 Evaluate side-chains 14 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 53 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 37 optimal weight: 0.0980 chunk 22 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.0170 chunk 21 optimal weight: 0.0980 chunk 9 optimal weight: 0.3980 chunk 29 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 49 optimal weight: 0.1980 overall best weight: 0.1018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.094502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.091066 restraints weight = 10444.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.091920 restraints weight = 7508.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.092575 restraints weight = 5517.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.093103 restraints weight = 4069.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.093436 restraints weight = 2993.172| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2770 moved from start: 0.8007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4880 Z= 0.128 Angle : 0.695 8.648 6580 Z= 0.356 Chirality : 0.046 0.146 748 Planarity : 0.004 0.026 836 Dihedral : 4.841 17.815 634 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.34), residues: 592 helix: -0.23 (0.30), residues: 294 sheet: -2.23 (0.67), residues: 56 loop : -1.34 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 233 TYR 0.010 0.001 TYR B 313 PHE 0.008 0.001 PHE C 90 TRP 0.004 0.001 TRP B 251 HIS 0.016 0.002 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 4880) covalent geometry : angle 0.69522 / 0.36 ( 6580) hydrogen bonds : bond 0.03596 / 2.42 ( 188) hydrogen bonds : angle 4.99118 / 3.57 ( 540) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 110 LYS cc_start: 0.6487 (pttt) cc_final: 0.6202 (tptt) REVERT: B 138 MET cc_start: 0.0411 (tpt) cc_final: -0.3254 (mtp) REVERT: B 153 MET cc_start: 0.6984 (mmp) cc_final: 0.6449 (mmp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0765 time to fit residues: 1.5290 Evaluate side-chains 12 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 0.0370 chunk 49 optimal weight: 0.4980 chunk 54 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 1.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 95 HIS ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.092398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.090157 restraints weight = 10861.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.090853 restraints weight = 7339.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.091345 restraints weight = 5020.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.091681 restraints weight = 3415.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.091911 restraints weight = 2320.782| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2824 moved from start: 0.8321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4880 Z= 0.135 Angle : 0.722 11.423 6580 Z= 0.363 Chirality : 0.047 0.315 748 Planarity : 0.004 0.024 836 Dihedral : 4.970 16.349 634 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.34), residues: 592 helix: -0.43 (0.29), residues: 304 sheet: -2.02 (0.71), residues: 56 loop : -1.26 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 233 TYR 0.014 0.001 TYR B 313 PHE 0.009 0.001 PHE B 314 TRP 0.009 0.001 TRP C 193 HIS 0.011 0.002 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 4880) covalent geometry : angle 0.72245 / 0.36 ( 6580) hydrogen bonds : bond 0.03482 / 2.31 ( 188) hydrogen bonds : angle 5.06714 / 3.62 ( 540) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: B 110 LYS cc_start: 0.6420 (pttt) cc_final: 0.6099 (tptt) REVERT: B 138 MET cc_start: 0.0750 (tpt) cc_final: -0.2840 (mtp) REVERT: B 153 MET cc_start: 0.6900 (mmp) cc_final: 0.6427 (mmp) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0804 time to fit residues: 1.5223 Evaluate side-chains 13 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 6.9990 chunk 19 optimal weight: 0.0370 chunk 56 optimal weight: 0.0670 chunk 24 optimal weight: 4.9990 chunk 55 optimal weight: 0.1980 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 48 optimal weight: 0.0030 overall best weight: 0.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 GLN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.093923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.091117 restraints weight = 11288.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.091843 restraints weight = 7830.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.092465 restraints weight = 5514.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.092842 restraints weight = 3887.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.093155 restraints weight = 2839.342| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2792 moved from start: 0.8510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4880 Z= 0.123 Angle : 0.698 10.964 6580 Z= 0.348 Chirality : 0.046 0.258 748 Planarity : 0.004 0.026 836 Dihedral : 4.816 17.586 634 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.35), residues: 592 helix: -0.28 (0.30), residues: 304 sheet: -2.19 (0.70), residues: 56 loop : -1.16 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 233 TYR 0.010 0.001 TYR B 313 PHE 0.007 0.001 PHE B 90 TRP 0.004 0.001 TRP B 251 HIS 0.009 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 4880) covalent geometry : angle 0.69772 / 0.35 ( 6580) hydrogen bonds : bond 0.03399 / 2.28 ( 188) hydrogen bonds : angle 4.84199 / 3.45 ( 540) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: B 110 LYS cc_start: 0.6519 (pttt) cc_final: 0.6221 (tptt) REVERT: B 138 MET cc_start: 0.0645 (tpt) cc_final: -0.2668 (mtp) REVERT: B 153 MET cc_start: 0.6839 (mmp) cc_final: 0.6467 (mmp) REVERT: B 233 ARG cc_start: 0.6245 (tpp80) cc_final: 0.5131 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0931 time to fit residues: 1.5965 Evaluate side-chains 12 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 42 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.092537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.090121 restraints weight = 10978.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.090848 restraints weight = 7227.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.091407 restraints weight = 4901.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.091758 restraints weight = 3321.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.091951 restraints weight = 2271.905| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2852 moved from start: 0.8731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4880 Z= 0.129 Angle : 0.722 10.359 6580 Z= 0.359 Chirality : 0.046 0.244 748 Planarity : 0.004 0.025 836 Dihedral : 4.847 16.991 634 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.34), residues: 592 helix: -0.36 (0.30), residues: 302 sheet: -2.16 (0.71), residues: 56 loop : -1.29 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 233 TYR 0.013 0.001 TYR B 313 PHE 0.008 0.001 PHE B 286 TRP 0.006 0.001 TRP B 193 HIS 0.008 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 4880) covalent geometry : angle 0.72181 / 0.36 ( 6580) hydrogen bonds : bond 0.03381 / 2.26 ( 188) hydrogen bonds : angle 5.05142 / 3.64 ( 540) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 110 LYS cc_start: 0.6414 (pttt) cc_final: 0.6136 (tptt) REVERT: B 138 MET cc_start: 0.0763 (tpt) cc_final: -0.2629 (mtp) REVERT: B 153 MET cc_start: 0.6884 (mmp) cc_final: 0.6603 (mmp) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0829 time to fit residues: 1.4455 Evaluate side-chains 12 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 49 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 0.0010 chunk 42 optimal weight: 0.0980 chunk 38 optimal weight: 0.0870 chunk 35 optimal weight: 0.0670 chunk 48 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.094129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.091564 restraints weight = 11346.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.092223 restraints weight = 8235.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.092636 restraints weight = 6043.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.093057 restraints weight = 4651.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.093333 restraints weight = 3418.710| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2739 moved from start: 0.8872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4880 Z= 0.124 Angle : 0.720 10.427 6580 Z= 0.353 Chirality : 0.046 0.235 748 Planarity : 0.004 0.025 836 Dihedral : 4.721 16.981 634 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.34), residues: 592 helix: -0.34 (0.30), residues: 304 sheet: -2.28 (0.70), residues: 56 loop : -1.28 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 233 TYR 0.010 0.001 TYR B 313 PHE 0.009 0.001 PHE B 90 TRP 0.004 0.001 TRP B 251 HIS 0.008 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 4880) covalent geometry : angle 0.71952 / 0.35 ( 6580) hydrogen bonds : bond 0.03441 / 2.32 ( 188) hydrogen bonds : angle 4.86941 / 3.49 ( 540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 892.63 seconds wall clock time: 16 minutes 18.63 seconds (978.63 seconds total)