Starting phenix.real_space_refine on Wed Sep 17 10:45:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kpd_62484/09_2025/9kpd_62484.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kpd_62484/09_2025/9kpd_62484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kpd_62484/09_2025/9kpd_62484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kpd_62484/09_2025/9kpd_62484.map" model { file = "/net/cci-nas-00/data/ceres_data/9kpd_62484/09_2025/9kpd_62484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kpd_62484/09_2025/9kpd_62484.cif" } resolution = 2.84 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= 0.001 sd= 0.021 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 53 5.16 5 C 5247 2.51 5 N 1419 2.21 5 O 1518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8237 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1961 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2231 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 7, 'TRANS': 262} Chain breaks: 1 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'SA0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.14, per 1000 atoms: 0.26 Number of scatterers: 8237 At special positions: 0 Unit cell: (76.96, 101.92, 132.08, 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 53 16.00 O 1518 8.00 N 1419 7.00 C 5247 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 69 " - pdb=" SG CYS R 79 " distance=2.01 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: 0.76 Conformation dependent library (CDL) restraints added in 436.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 10 sheets defined 42.6% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.676A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.514A pdb=" N HIS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.634A pdb=" N ASN A 104 " --> pdb=" O GLN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 133 Processing helix chain 'A' and resid 148 through 158 removed outlier: 3.718A pdb=" N ALA A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 207 removed outlier: 4.275A pdb=" N SER A 207 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 247 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.537A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 39 Processing helix chain 'R' and resid 43 through 71 removed outlier: 3.536A pdb=" N MET R 64 " --> pdb=" O GLN R 60 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE R 68 " --> pdb=" O MET R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 107 removed outlier: 3.551A pdb=" N TRP R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN R 96 " --> pdb=" O THR R 92 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER R 97 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL R 107 " --> pdb=" O TYR R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 125 removed outlier: 3.518A pdb=" N LEU R 125 " --> pdb=" O ARG R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 141 removed outlier: 4.095A pdb=" N LEU R 134 " --> pdb=" O LEU R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 156 Processing helix chain 'R' and resid 173 through 210 removed outlier: 4.073A pdb=" N GLN R 177 " --> pdb=" O PHE R 173 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N THR R 182 " --> pdb=" O PHE R 178 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU R 185 " --> pdb=" O HIS R 181 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE R 187 " --> pdb=" O VAL R 183 " (cutoff:3.500A) Proline residue: R 188 - end of helix Processing helix chain 'R' and resid 211 through 214 Processing helix chain 'R' and resid 215 through 249 Processing helix chain 'R' and resid 258 through 280 Processing helix chain 'R' and resid 280 through 285 removed outlier: 3.918A pdb=" N LYS R 284 " --> pdb=" O SER R 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 79 removed outlier: 6.440A pdb=" N HIS A 41 " --> pdb=" O HIS A 85 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N PHE A 87 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU A 43 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL A 89 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N LEU A 45 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 108 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE A 109 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N PHE A 145 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE A 111 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN A 147 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 113 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL A 142 " --> pdb=" O TYR A 215 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.303A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.734A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.582A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.434A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.772A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.610A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.666A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.799A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1326 1.29 - 1.42: 2327 1.42 - 1.56: 4686 1.56 - 1.70: 0 1.70 - 1.84: 75 Bond restraints: 8414 Sorted by residual: bond pdb=" CA PHE R 240 " pdb=" C PHE R 240 " ideal model delta sigma weight residual 1.524 1.412 0.111 1.37e-02 5.33e+03 6.57e+01 bond pdb=" C THR R 224 " pdb=" O THR R 224 " ideal model delta sigma weight residual 1.236 1.147 0.090 1.15e-02 7.56e+03 6.08e+01 bond pdb=" C VAL R 101 " pdb=" O VAL R 101 " ideal model delta sigma weight residual 1.237 1.146 0.091 1.23e-02 6.61e+03 5.50e+01 bond pdb=" CA LEU R 99 " pdb=" C LEU R 99 " ideal model delta sigma weight residual 1.524 1.436 0.088 1.24e-02 6.50e+03 5.08e+01 bond pdb=" CA TYR R 71 " pdb=" C TYR R 71 " ideal model delta sigma weight residual 1.524 1.437 0.087 1.26e-02 6.30e+03 4.72e+01 ... (remaining 8409 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 11139 3.36 - 6.72: 219 6.72 - 10.08: 37 10.08 - 13.43: 6 13.43 - 16.79: 1 Bond angle restraints: 11402 Sorted by residual: angle pdb=" N PHE R 240 " pdb=" CA PHE R 240 " pdb=" C PHE R 240 " ideal model delta sigma weight residual 112.45 101.35 11.10 1.39e+00 5.18e-01 6.37e+01 angle pdb=" N ASN R 66 " pdb=" CA ASN R 66 " pdb=" C ASN R 66 " ideal model delta sigma weight residual 111.14 119.46 -8.32 1.08e+00 8.57e-01 5.94e+01 angle pdb=" C SER R 280 " pdb=" N PRO R 281 " pdb=" CA PRO R 281 " ideal model delta sigma weight residual 119.84 129.22 -9.38 1.25e+00 6.40e-01 5.63e+01 angle pdb=" N LEU R 229 " pdb=" CA LEU R 229 " pdb=" C LEU R 229 " ideal model delta sigma weight residual 111.36 103.29 8.07 1.09e+00 8.42e-01 5.49e+01 angle pdb=" CA ILE R 142 " pdb=" C ILE R 142 " pdb=" N PRO R 143 " ideal model delta sigma weight residual 120.83 116.37 4.46 6.10e-01 2.69e+00 5.34e+01 ... (remaining 11397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4362 17.38 - 34.77: 469 34.77 - 52.15: 139 52.15 - 69.53: 23 69.53 - 86.91: 9 Dihedral angle restraints: 5002 sinusoidal: 1991 harmonic: 3011 Sorted by residual: dihedral pdb=" CB CYS R 69 " pdb=" SG CYS R 69 " pdb=" SG CYS R 79 " pdb=" CB CYS R 79 " ideal model delta sinusoidal sigma weight residual 93.00 24.10 68.90 1 1.00e+01 1.00e-02 6.14e+01 dihedral pdb=" C THR R 204 " pdb=" N THR R 204 " pdb=" CA THR R 204 " pdb=" CB THR R 204 " ideal model delta harmonic sigma weight residual -122.00 -140.45 18.45 0 2.50e+00 1.60e-01 5.45e+01 dihedral pdb=" N THR R 204 " pdb=" C THR R 204 " pdb=" CA THR R 204 " pdb=" CB THR R 204 " ideal model delta harmonic sigma weight residual 123.40 138.03 -14.63 0 2.50e+00 1.60e-01 3.42e+01 ... (remaining 4999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 1231 0.154 - 0.308: 41 0.308 - 0.463: 14 0.463 - 0.617: 6 0.617 - 0.771: 1 Chirality restraints: 1293 Sorted by residual: chirality pdb=" CA THR R 204 " pdb=" N THR R 204 " pdb=" C THR R 204 " pdb=" CB THR R 204 " both_signs ideal model delta sigma weight residual False 2.53 1.76 0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" CA VAL R 265 " pdb=" N VAL R 265 " pdb=" C VAL R 265 " pdb=" CB VAL R 265 " both_signs ideal model delta sigma weight residual False 2.44 1.83 0.61 2.00e-01 2.50e+01 9.23e+00 chirality pdb=" CA MET R 64 " pdb=" N MET R 64 " pdb=" C MET R 64 " pdb=" CB MET R 64 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.55e+00 ... (remaining 1290 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 234 " -0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C ILE R 234 " 0.075 2.00e-02 2.50e+03 pdb=" O ILE R 234 " -0.028 2.00e-02 2.50e+03 pdb=" N VAL R 235 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 56 " 0.019 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C ARG R 56 " -0.070 2.00e-02 2.50e+03 pdb=" O ARG R 56 " 0.027 2.00e-02 2.50e+03 pdb=" N PHE R 57 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 139 " 0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C VAL R 139 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL R 139 " 0.025 2.00e-02 2.50e+03 pdb=" N THR R 140 " 0.023 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 135 2.58 - 3.16: 7236 3.16 - 3.74: 13805 3.74 - 4.32: 18931 4.32 - 4.90: 30991 Nonbonded interactions: 71098 Sorted by model distance: nonbonded pdb=" O ALA R 62 " pdb=" ND2 ASN R 66 " model vdw 2.003 3.120 nonbonded pdb=" OG SER N 7 " pdb=" OG SER N 21 " model vdw 2.209 3.040 nonbonded pdb=" O LYS R 254 " pdb=" N LEU R 258 " model vdw 2.209 3.120 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.217 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.220 3.040 ... (remaining 71093 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.660 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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 0.111 8417 Z= 0.802 Angle : 1.085 16.793 11408 Z= 0.692 Chirality : 0.083 0.771 1293 Planarity : 0.006 0.073 1440 Dihedral : 16.050 86.913 3041 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 26.15 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.31 % Favored : 95.20 % Rotamer: Outliers : 2.56 % Allowed : 23.44 % Favored : 74.00 % Cbeta Deviations : 0.31 % 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 aren not related in a simple way. whole: 0.01 (0.26), residues: 1021 helix: 1.07 (0.26), residues: 410 sheet: -0.04 (0.33), residues: 229 loop : -1.06 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 13 TYR 0.032 0.002 TYR A 194 PHE 0.050 0.002 PHE R 240 TRP 0.048 0.003 TRP R 120 HIS 0.009 0.001 HIS R 181 Details of bonding type rmsd covalent geometry : bond 0.01163 ( 8414) covalent geometry : angle 1.08119 (11402) SS BOND : bond 0.01445 ( 3) SS BOND : angle 4.21697 ( 6) hydrogen bonds : bond 0.17494 ( 443) hydrogen bonds : angle 6.64215 ( 1278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 216 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8319 (p) cc_final: 0.7973 (t) REVERT: A 202 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7626 (ttp-110) REVERT: N 72 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.6613 (ttm-80) REVERT: N 87 LYS cc_start: 0.8088 (mtmt) cc_final: 0.7760 (mtmm) REVERT: R 92 THR cc_start: 0.6772 (OUTLIER) cc_final: 0.6221 (m) REVERT: R 192 PHE cc_start: 0.7690 (t80) cc_final: 0.7335 (t80) REVERT: R 219 MET cc_start: 0.5470 (mmm) cc_final: 0.5238 (mmm) REVERT: R 276 LEU cc_start: 0.7484 (mm) cc_final: 0.7233 (tm) outliers start: 23 outliers final: 8 residues processed: 234 average time/residue: 0.6715 time to fit residues: 165.3599 Evaluate side-chains 217 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 61 TRP Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 171 GLU Chi-restraints excluded: chain R residue 174 HIS Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 240 PHE Chi-restraints excluded: chain R residue 265 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 92 GLN A 149 GLN B 17 GLN N 35 ASN R 60 GLN R 89 ASN ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 GLN R 179 GLN R 209 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.160783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.132750 restraints weight = 11804.037| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.92 r_work: 0.3555 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8417 Z= 0.175 Angle : 0.615 9.820 11408 Z= 0.327 Chirality : 0.043 0.145 1293 Planarity : 0.004 0.050 1440 Dihedral : 6.140 80.484 1166 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.00 % Allowed : 20.22 % Favored : 74.78 % 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 aren not related in a simple way. whole: 0.40 (0.26), residues: 1021 helix: 1.76 (0.24), residues: 414 sheet: -0.07 (0.33), residues: 229 loop : -1.19 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 13 TYR 0.026 0.002 TYR A 194 PHE 0.017 0.002 PHE R 68 TRP 0.025 0.002 TRP R 120 HIS 0.003 0.001 HIS R 209 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8414) covalent geometry : angle 0.60749 (11402) SS BOND : bond 0.00329 ( 3) SS BOND : angle 4.25292 ( 6) hydrogen bonds : bond 0.04624 ( 443) hydrogen bonds : angle 4.55747 ( 1278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 139 THR cc_start: 0.8388 (p) cc_final: 0.8025 (t) REVERT: A 145 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7861 (t80) REVERT: A 198 ASP cc_start: 0.7237 (m-30) cc_final: 0.6814 (m-30) REVERT: A 211 ARG cc_start: 0.7630 (mtm-85) cc_final: 0.7378 (mtm-85) REVERT: B 219 ARG cc_start: 0.8472 (mtp85) cc_final: 0.8200 (mtp85) REVERT: B 269 ILE cc_start: 0.8758 (mt) cc_final: 0.8500 (mm) REVERT: B 314 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7664 (ttm170) REVERT: N 83 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.6556 (mtm) REVERT: R 122 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6540 (mp) REVERT: R 192 PHE cc_start: 0.7470 (t80) cc_final: 0.6860 (t80) REVERT: R 243 ILE cc_start: 0.6326 (OUTLIER) cc_final: 0.6110 (mm) REVERT: R 252 PHE cc_start: 0.4362 (OUTLIER) cc_final: 0.3136 (m-80) REVERT: R 262 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6567 (tp30) REVERT: R 271 MET cc_start: 0.7110 (mtp) cc_final: 0.6855 (mtp) outliers start: 45 outliers final: 17 residues processed: 259 average time/residue: 0.5513 time to fit residues: 151.3430 Evaluate side-chains 242 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 61 TRP Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 252 PHE Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 261 TRP Chi-restraints excluded: chain R residue 262 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 27 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.0670 chunk 86 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 55 optimal weight: 0.0980 chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 92 GLN A 149 GLN A 217 HIS A 226 ASN B 17 GLN B 110 ASN B 125 ASN ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.160817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.132927 restraints weight = 11723.974| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.90 r_work: 0.3556 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8417 Z= 0.158 Angle : 0.566 9.381 11408 Z= 0.298 Chirality : 0.042 0.137 1293 Planarity : 0.004 0.055 1440 Dihedral : 5.314 76.595 1150 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.33 % Favored : 96.57 % Rotamer: Outliers : 5.22 % Allowed : 20.44 % Favored : 74.33 % 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 aren not related in a simple way. whole: 0.67 (0.26), residues: 1021 helix: 2.10 (0.24), residues: 414 sheet: -0.15 (0.33), residues: 234 loop : -1.04 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 13 TYR 0.025 0.001 TYR A 194 PHE 0.013 0.002 PHE R 88 TRP 0.028 0.002 TRP R 120 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8414) covalent geometry : angle 0.56285 (11402) SS BOND : bond 0.00604 ( 3) SS BOND : angle 2.64640 ( 6) hydrogen bonds : bond 0.04251 ( 443) hydrogen bonds : angle 4.23354 ( 1278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 228 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8382 (p) cc_final: 0.8004 (t) REVERT: A 145 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.7832 (t80) REVERT: A 198 ASP cc_start: 0.7154 (m-30) cc_final: 0.6768 (m-30) REVERT: B 219 ARG cc_start: 0.8416 (mtp85) cc_final: 0.8136 (mtp85) REVERT: B 228 ASP cc_start: 0.7798 (p0) cc_final: 0.7590 (p0) REVERT: B 264 TYR cc_start: 0.8631 (m-80) cc_final: 0.8368 (m-80) REVERT: B 314 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7694 (ttm170) REVERT: N 34 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7933 (mtm) REVERT: R 22 ILE cc_start: 0.6929 (mm) cc_final: 0.6640 (mm) REVERT: R 61 TRP cc_start: 0.5524 (m100) cc_final: 0.5242 (m100) REVERT: R 241 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6378 (mp) REVERT: R 244 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6909 (mm) REVERT: R 252 PHE cc_start: 0.4222 (OUTLIER) cc_final: 0.3147 (m-80) REVERT: R 262 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6541 (tp30) REVERT: R 268 PHE cc_start: 0.6171 (m-80) cc_final: 0.5549 (t80) REVERT: R 271 MET cc_start: 0.7185 (mtp) cc_final: 0.6933 (mtp) outliers start: 47 outliers final: 19 residues processed: 254 average time/residue: 0.5584 time to fit residues: 150.1284 Evaluate side-chains 243 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain R residue 47 MET Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 252 PHE Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 261 TRP Chi-restraints excluded: chain R residue 262 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 59 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 134 ASN A 149 GLN A 226 ASN B 17 GLN B 88 ASN B 110 ASN B 125 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 GLN R 89 ASN ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.159618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.131726 restraints weight = 11843.981| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.91 r_work: 0.3550 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8417 Z= 0.169 Angle : 0.562 9.414 11408 Z= 0.296 Chirality : 0.042 0.138 1293 Planarity : 0.004 0.055 1440 Dihedral : 4.752 69.720 1146 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.13 % Favored : 96.77 % Rotamer: Outliers : 4.78 % Allowed : 22.33 % Favored : 72.89 % 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 aren not related in a simple way. whole: 0.57 (0.26), residues: 1021 helix: 2.13 (0.24), residues: 412 sheet: -0.42 (0.32), residues: 236 loop : -1.06 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 13 TYR 0.025 0.001 TYR A 194 PHE 0.016 0.002 PHE A 84 TRP 0.028 0.002 TRP R 120 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8414) covalent geometry : angle 0.55913 (11402) SS BOND : bond 0.00444 ( 3) SS BOND : angle 2.39328 ( 6) hydrogen bonds : bond 0.04150 ( 443) hydrogen bonds : angle 4.13988 ( 1278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7275 (mt-10) REVERT: A 139 THR cc_start: 0.8459 (p) cc_final: 0.8070 (t) REVERT: A 145 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.7847 (t80) REVERT: A 198 ASP cc_start: 0.7167 (m-30) cc_final: 0.6811 (m-30) REVERT: A 211 ARG cc_start: 0.7632 (mtm-85) cc_final: 0.7335 (mtm-85) REVERT: B 219 ARG cc_start: 0.8469 (mtp85) cc_final: 0.8218 (mtp85) REVERT: B 228 ASP cc_start: 0.7753 (p0) cc_final: 0.7493 (p0) REVERT: B 258 ASP cc_start: 0.7816 (t0) cc_final: 0.7612 (t0) REVERT: B 314 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7710 (ttm170) REVERT: G 27 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8204 (mtp85) REVERT: N 34 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7900 (mtm) REVERT: R 22 ILE cc_start: 0.6964 (mm) cc_final: 0.6693 (mm) REVERT: R 61 TRP cc_start: 0.5523 (m100) cc_final: 0.5315 (m100) REVERT: R 90 ILE cc_start: 0.6499 (mm) cc_final: 0.6214 (mm) REVERT: R 241 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6566 (mp) REVERT: R 243 ILE cc_start: 0.6303 (mm) cc_final: 0.5453 (mt) REVERT: R 244 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7063 (mm) REVERT: R 252 PHE cc_start: 0.4459 (OUTLIER) cc_final: 0.3636 (m-80) REVERT: R 262 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6595 (tp30) REVERT: R 271 MET cc_start: 0.7218 (mtp) cc_final: 0.6961 (mtp) outliers start: 43 outliers final: 19 residues processed: 249 average time/residue: 0.5652 time to fit residues: 149.1844 Evaluate side-chains 249 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 222 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 252 PHE Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 261 TRP Chi-restraints excluded: chain R residue 262 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 97 optimal weight: 0.0030 chunk 56 optimal weight: 0.6980 chunk 81 optimal weight: 0.0070 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 91 optimal weight: 0.2980 chunk 39 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 overall best weight: 0.3208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 92 GLN A 149 GLN A 226 ASN B 17 GLN B 88 ASN B 110 ASN B 125 ASN ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.161554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.133918 restraints weight = 11777.852| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.92 r_work: 0.3565 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8417 Z= 0.128 Angle : 0.540 9.899 11408 Z= 0.284 Chirality : 0.041 0.159 1293 Planarity : 0.004 0.055 1440 Dihedral : 4.603 65.067 1146 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 4.56 % Allowed : 23.11 % Favored : 72.33 % 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 aren not related in a simple way. whole: 0.70 (0.26), residues: 1021 helix: 2.27 (0.25), residues: 414 sheet: -0.46 (0.32), residues: 236 loop : -0.99 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 13 TYR 0.019 0.001 TYR A 194 PHE 0.011 0.001 PHE R 126 TRP 0.017 0.002 TRP R 120 HIS 0.003 0.001 HIS R 181 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8414) covalent geometry : angle 0.53806 (11402) SS BOND : bond 0.00542 ( 3) SS BOND : angle 1.80994 ( 6) hydrogen bonds : bond 0.03867 ( 443) hydrogen bonds : angle 4.01808 ( 1278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8386 (p) cc_final: 0.7998 (t) REVERT: A 145 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7881 (t80) REVERT: A 198 ASP cc_start: 0.7113 (m-30) cc_final: 0.6697 (m-30) REVERT: B 219 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8183 (mtp85) REVERT: B 254 ASP cc_start: 0.7677 (t0) cc_final: 0.7461 (t0) REVERT: B 258 ASP cc_start: 0.7867 (t0) cc_final: 0.7594 (t0) REVERT: B 314 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7676 (ttm170) REVERT: G 27 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8124 (mtp85) REVERT: N 34 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7842 (mtm) REVERT: N 36 TRP cc_start: 0.8743 (m100) cc_final: 0.8398 (m100) REVERT: R 90 ILE cc_start: 0.6440 (mm) cc_final: 0.6154 (mm) REVERT: R 105 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7500 (tp) REVERT: R 107 VAL cc_start: 0.7740 (OUTLIER) cc_final: 0.7460 (m) REVERT: R 121 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6408 (mmt-90) REVERT: R 122 ILE cc_start: 0.6501 (OUTLIER) cc_final: 0.6254 (mp) REVERT: R 243 ILE cc_start: 0.6278 (mm) cc_final: 0.5444 (mt) REVERT: R 244 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.7053 (mm) REVERT: R 252 PHE cc_start: 0.4349 (OUTLIER) cc_final: 0.3630 (m-80) REVERT: R 268 PHE cc_start: 0.6074 (m-80) cc_final: 0.5517 (t80) REVERT: R 271 MET cc_start: 0.7114 (mtp) cc_final: 0.6846 (mtp) outliers start: 41 outliers final: 16 residues processed: 252 average time/residue: 0.5943 time to fit residues: 158.4697 Evaluate side-chains 245 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 252 PHE Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 261 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 0.0970 chunk 42 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 149 GLN A 226 ASN B 17 GLN B 88 ASN B 110 ASN B 125 ASN R 112 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.160027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.132694 restraints weight = 11738.359| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.88 r_work: 0.3552 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8417 Z= 0.169 Angle : 0.580 15.200 11408 Z= 0.301 Chirality : 0.042 0.162 1293 Planarity : 0.004 0.055 1440 Dihedral : 4.593 56.615 1146 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.38 % Rotamer: Outliers : 4.56 % Allowed : 23.67 % Favored : 71.78 % 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 aren not related in a simple way. whole: 0.66 (0.26), residues: 1021 helix: 2.23 (0.25), residues: 411 sheet: -0.45 (0.32), residues: 236 loop : -0.99 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 13 TYR 0.026 0.002 TYR R 266 PHE 0.028 0.002 PHE R 57 TRP 0.020 0.002 TRP R 120 HIS 0.002 0.001 HIS R 181 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8414) covalent geometry : angle 0.57847 (11402) SS BOND : bond 0.00579 ( 3) SS BOND : angle 1.62250 ( 6) hydrogen bonds : bond 0.04034 ( 443) hydrogen bonds : angle 4.04234 ( 1278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8439 (p) cc_final: 0.8056 (t) REVERT: A 145 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7849 (t80) REVERT: A 198 ASP cc_start: 0.7172 (m-30) cc_final: 0.6825 (m-30) REVERT: B 219 ARG cc_start: 0.8460 (mtp85) cc_final: 0.8181 (mtp85) REVERT: B 258 ASP cc_start: 0.7831 (t0) cc_final: 0.7598 (t0) REVERT: B 314 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7728 (ttm170) REVERT: G 27 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8235 (mtp85) REVERT: N 34 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7859 (mtm) REVERT: N 36 TRP cc_start: 0.8740 (m100) cc_final: 0.8342 (m100) REVERT: R 90 ILE cc_start: 0.6478 (mm) cc_final: 0.6179 (mm) REVERT: R 107 VAL cc_start: 0.7743 (OUTLIER) cc_final: 0.7447 (m) REVERT: R 219 MET cc_start: 0.5463 (mmm) cc_final: 0.5184 (mmm) REVERT: R 243 ILE cc_start: 0.6415 (mm) cc_final: 0.5550 (mt) REVERT: R 262 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6427 (tp30) REVERT: R 271 MET cc_start: 0.7160 (mtp) cc_final: 0.6871 (mtp) outliers start: 41 outliers final: 22 residues processed: 246 average time/residue: 0.6003 time to fit residues: 156.2308 Evaluate side-chains 248 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 252 PHE Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 261 TRP Chi-restraints excluded: chain R residue 262 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 59 optimal weight: 0.0570 chunk 100 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 92 GLN A 122 GLN A 126 ASN A 149 GLN A 226 ASN B 17 GLN B 88 ASN B 110 ASN B 125 ASN B 340 ASN R 181 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.160342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.132896 restraints weight = 11723.261| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.89 r_work: 0.3554 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8417 Z= 0.162 Angle : 0.569 9.913 11408 Z= 0.298 Chirality : 0.042 0.165 1293 Planarity : 0.004 0.055 1440 Dihedral : 4.510 48.872 1146 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.04 % Favored : 96.87 % Rotamer: Outliers : 4.33 % Allowed : 24.89 % Favored : 70.78 % 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 aren not related in a simple way. whole: 0.62 (0.26), residues: 1021 helix: 2.18 (0.24), residues: 412 sheet: -0.43 (0.32), residues: 235 loop : -1.02 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 13 TYR 0.024 0.002 TYR A 194 PHE 0.028 0.002 PHE R 192 TRP 0.027 0.002 TRP R 120 HIS 0.003 0.001 HIS R 181 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8414) covalent geometry : angle 0.56824 (11402) SS BOND : bond 0.00602 ( 3) SS BOND : angle 1.52841 ( 6) hydrogen bonds : bond 0.03983 ( 443) hydrogen bonds : angle 4.01320 ( 1278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7337 (mm-30) REVERT: A 139 THR cc_start: 0.8377 (p) cc_final: 0.7982 (t) REVERT: A 145 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7873 (t80) REVERT: A 198 ASP cc_start: 0.7171 (m-30) cc_final: 0.6814 (m-30) REVERT: B 219 ARG cc_start: 0.8506 (mtp85) cc_final: 0.8200 (mtp85) REVERT: B 258 ASP cc_start: 0.7830 (t0) cc_final: 0.7610 (t0) REVERT: B 314 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7723 (ttm170) REVERT: G 27 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8207 (mtp85) REVERT: N 34 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7838 (mtm) REVERT: N 36 TRP cc_start: 0.8704 (m100) cc_final: 0.8355 (m100) REVERT: R 90 ILE cc_start: 0.6511 (mm) cc_final: 0.6201 (mm) REVERT: R 107 VAL cc_start: 0.7745 (OUTLIER) cc_final: 0.7485 (m) REVERT: R 219 MET cc_start: 0.5473 (mmm) cc_final: 0.5109 (mmm) REVERT: R 262 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6527 (tp30) REVERT: R 268 PHE cc_start: 0.6057 (m-80) cc_final: 0.5412 (t80) REVERT: R 271 MET cc_start: 0.7217 (mtp) cc_final: 0.6908 (mtp) outliers start: 39 outliers final: 22 residues processed: 227 average time/residue: 0.6065 time to fit residues: 145.6044 Evaluate side-chains 230 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 252 PHE Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 261 TRP Chi-restraints excluded: chain R residue 262 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 27 optimal weight: 0.0370 chunk 8 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 51 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 91 optimal weight: 0.0670 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN B 75 GLN B 110 ASN B 125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.161533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.134235 restraints weight = 11690.947| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.89 r_work: 0.3577 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8417 Z= 0.121 Angle : 0.548 10.204 11408 Z= 0.286 Chirality : 0.041 0.159 1293 Planarity : 0.004 0.056 1440 Dihedral : 4.332 41.289 1146 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.13 % Favored : 96.77 % Rotamer: Outliers : 4.22 % Allowed : 25.22 % Favored : 70.56 % 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 aren not related in a simple way. whole: 0.70 (0.26), residues: 1021 helix: 2.36 (0.24), residues: 416 sheet: -0.50 (0.32), residues: 231 loop : -1.09 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 13 TYR 0.022 0.001 TYR R 266 PHE 0.026 0.002 PHE R 240 TRP 0.027 0.002 TRP R 120 HIS 0.002 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8414) covalent geometry : angle 0.54777 (11402) SS BOND : bond 0.00479 ( 3) SS BOND : angle 1.28265 ( 6) hydrogen bonds : bond 0.03747 ( 443) hydrogen bonds : angle 3.91710 ( 1278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7326 (mm-30) REVERT: A 139 THR cc_start: 0.8359 (p) cc_final: 0.7971 (t) REVERT: A 145 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7900 (t80) REVERT: B 219 ARG cc_start: 0.8515 (mtp85) cc_final: 0.8238 (mtp85) REVERT: B 314 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7688 (ttm170) REVERT: N 34 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7782 (mtm) REVERT: N 36 TRP cc_start: 0.8629 (m100) cc_final: 0.8382 (m100) REVERT: R 90 ILE cc_start: 0.6472 (mm) cc_final: 0.6125 (mm) REVERT: R 105 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7596 (tp) REVERT: R 107 VAL cc_start: 0.7802 (OUTLIER) cc_final: 0.7563 (m) REVERT: R 193 LEU cc_start: 0.7605 (tp) cc_final: 0.7352 (tm) REVERT: R 219 MET cc_start: 0.5545 (mmm) cc_final: 0.5182 (mmm) REVERT: R 271 MET cc_start: 0.7107 (mtp) cc_final: 0.6819 (mtp) outliers start: 38 outliers final: 19 residues processed: 231 average time/residue: 0.5997 time to fit residues: 146.4558 Evaluate side-chains 231 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 252 PHE Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 261 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN B 110 ASN B 125 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.159513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.132126 restraints weight = 11603.551| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.89 r_work: 0.3546 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8417 Z= 0.189 Angle : 0.588 11.545 11408 Z= 0.306 Chirality : 0.043 0.180 1293 Planarity : 0.004 0.055 1440 Dihedral : 4.420 33.118 1146 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.33 % Favored : 96.57 % Rotamer: Outliers : 3.56 % Allowed : 26.00 % Favored : 70.44 % 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 aren not related in a simple way. whole: 0.69 (0.26), residues: 1021 helix: 2.23 (0.24), residues: 412 sheet: -0.39 (0.32), residues: 241 loop : -0.98 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 13 TYR 0.024 0.002 TYR A 194 PHE 0.030 0.002 PHE R 192 TRP 0.031 0.002 TRP R 120 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 8414) covalent geometry : angle 0.58756 (11402) SS BOND : bond 0.00520 ( 3) SS BOND : angle 1.49196 ( 6) hydrogen bonds : bond 0.03968 ( 443) hydrogen bonds : angle 4.00312 ( 1278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7363 (mm-30) REVERT: A 139 THR cc_start: 0.8396 (p) cc_final: 0.7995 (t) REVERT: A 145 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.7867 (t80) REVERT: A 198 ASP cc_start: 0.7197 (m-30) cc_final: 0.6817 (m-30) REVERT: A 202 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7731 (ttp-110) REVERT: B 10 GLU cc_start: 0.7964 (tp30) cc_final: 0.7748 (tp30) REVERT: B 219 ARG cc_start: 0.8516 (mtp85) cc_final: 0.8230 (mtp85) REVERT: B 228 ASP cc_start: 0.7666 (p0) cc_final: 0.7451 (p0) REVERT: B 314 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7768 (ttm170) REVERT: N 34 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7861 (mtm) REVERT: N 36 TRP cc_start: 0.8701 (m100) cc_final: 0.8358 (m100) REVERT: R 90 ILE cc_start: 0.6577 (mm) cc_final: 0.6232 (mm) REVERT: R 107 VAL cc_start: 0.7822 (OUTLIER) cc_final: 0.7586 (m) REVERT: R 193 LEU cc_start: 0.7590 (tp) cc_final: 0.7328 (tm) REVERT: R 219 MET cc_start: 0.5563 (mmm) cc_final: 0.5218 (mmm) REVERT: R 262 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6578 (tp30) REVERT: R 271 MET cc_start: 0.7158 (mtp) cc_final: 0.6867 (mtp) outliers start: 32 outliers final: 18 residues processed: 232 average time/residue: 0.6066 time to fit residues: 148.5967 Evaluate side-chains 240 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 252 PHE Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 262 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 56 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 91 optimal weight: 0.0070 chunk 28 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 92 GLN A 122 GLN A 126 ASN A 149 GLN A 226 ASN B 17 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 125 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.159882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.132655 restraints weight = 11580.136| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.88 r_work: 0.3552 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8417 Z= 0.170 Angle : 0.592 12.200 11408 Z= 0.308 Chirality : 0.043 0.177 1293 Planarity : 0.004 0.056 1440 Dihedral : 4.360 26.672 1146 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.13 % Favored : 96.77 % Rotamer: Outliers : 3.00 % Allowed : 27.33 % Favored : 69.67 % 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 aren not related in a simple way. whole: 0.68 (0.26), residues: 1021 helix: 2.22 (0.24), residues: 414 sheet: -0.44 (0.32), residues: 239 loop : -0.98 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 13 TYR 0.022 0.002 TYR A 194 PHE 0.029 0.002 PHE R 102 TRP 0.041 0.002 TRP R 261 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8414) covalent geometry : angle 0.59145 (11402) SS BOND : bond 0.00486 ( 3) SS BOND : angle 1.37965 ( 6) hydrogen bonds : bond 0.03942 ( 443) hydrogen bonds : angle 3.99990 ( 1278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7343 (mm-30) REVERT: A 139 THR cc_start: 0.8360 (p) cc_final: 0.7967 (t) REVERT: A 145 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7852 (t80) REVERT: A 198 ASP cc_start: 0.7172 (m-30) cc_final: 0.6788 (m-30) REVERT: A 202 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7803 (ttp-110) REVERT: B 10 GLU cc_start: 0.7965 (tp30) cc_final: 0.7748 (tp30) REVERT: B 219 ARG cc_start: 0.8509 (mtp85) cc_final: 0.8216 (mtp85) REVERT: B 314 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7716 (ttm170) REVERT: N 34 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7870 (mtm) REVERT: N 36 TRP cc_start: 0.8673 (m100) cc_final: 0.8349 (m100) REVERT: R 107 VAL cc_start: 0.7826 (OUTLIER) cc_final: 0.7598 (m) REVERT: R 219 MET cc_start: 0.5598 (mmm) cc_final: 0.5254 (mmm) REVERT: R 262 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6569 (tp30) REVERT: R 271 MET cc_start: 0.7086 (mtp) cc_final: 0.6820 (mtp) outliers start: 27 outliers final: 18 residues processed: 229 average time/residue: 0.6028 time to fit residues: 145.6213 Evaluate side-chains 231 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 252 PHE Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 262 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 72 optimal weight: 0.0270 chunk 32 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 chunk 47 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 63 optimal weight: 0.0770 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 149 GLN A 217 HIS A 226 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 125 ASN B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.161383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.134109 restraints weight = 11709.617| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.91 r_work: 0.3582 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8417 Z= 0.119 Angle : 0.563 12.714 11408 Z= 0.293 Chirality : 0.042 0.166 1293 Planarity : 0.004 0.056 1440 Dihedral : 4.168 24.201 1146 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.74 % Favored : 97.16 % Rotamer: Outliers : 2.89 % Allowed : 27.33 % Favored : 69.78 % 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 aren not related in a simple way. whole: 0.76 (0.26), residues: 1021 helix: 2.34 (0.24), residues: 419 sheet: -0.37 (0.32), residues: 233 loop : -1.06 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 13 TYR 0.023 0.001 TYR R 266 PHE 0.030 0.002 PHE R 102 TRP 0.028 0.002 TRP R 120 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8414) covalent geometry : angle 0.56239 (11402) SS BOND : bond 0.00384 ( 3) SS BOND : angle 1.24775 ( 6) hydrogen bonds : bond 0.03667 ( 443) hydrogen bonds : angle 3.88907 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3926.70 seconds wall clock time: 67 minutes 38.67 seconds (4058.67 seconds total)