Starting phenix.real_space_refine on Tue Apr 29 00:16:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kpd_62484/04_2025/9kpd_62484.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kpd_62484/04_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_62484/04_2025/9kpd_62484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kpd_62484/04_2025/9kpd_62484.map" model { file = "/net/cci-nas-00/data/ceres_data/9kpd_62484/04_2025/9kpd_62484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kpd_62484/04_2025/9kpd_62484.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.75, per 1000 atoms: 0.70 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: 2.58 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.18 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: 2.60 Time building geometry restraints manager: 2.88 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.430 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.630 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 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 TRP 0.048 0.003 TRP R 120 HIS 0.009 0.001 HIS R 181 PHE 0.050 0.002 PHE R 240 TYR 0.032 0.002 TYR A 194 ARG 0.009 0.001 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.17494 ( 443) hydrogen bonds : angle 6.64215 ( 1278) SS BOND : bond 0.01445 ( 3) SS BOND : angle 4.21697 ( 6) covalent geometry : bond 0.01163 ( 8414) covalent geometry : angle 1.08119 (11402) *********************** 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 : 0.815 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: 1.2434 time to fit residues: 306.9012 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 : 0.805 ------------------------------------------------------------------------------- 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 85 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.0070 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 B 220 GLN N 35 ASN R 60 GLN R 89 ASN ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 151 GLN R 177 GLN R 179 GLN R 209 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.160388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.132485 restraints weight = 11678.785| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.90 r_work: 0.3550 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8417 Z= 0.193 Angle : 0.628 10.088 11408 Z= 0.333 Chirality : 0.044 0.154 1293 Planarity : 0.004 0.050 1440 Dihedral : 6.186 80.128 1166 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.89 % Allowed : 20.89 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1021 helix: 1.78 (0.24), residues: 411 sheet: -0.06 (0.33), residues: 229 loop : -1.21 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 120 HIS 0.003 0.001 HIS R 209 PHE 0.017 0.002 PHE R 68 TYR 0.030 0.002 TYR A 194 ARG 0.006 0.001 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.04658 ( 443) hydrogen bonds : angle 4.59028 ( 1278) SS BOND : bond 0.00745 ( 3) SS BOND : angle 4.50156 ( 6) covalent geometry : bond 0.00423 ( 8414) covalent geometry : angle 0.61995 (11402) *********************** 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 274 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 230 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 139 THR cc_start: 0.8396 (p) cc_final: 0.8029 (t) REVERT: A 145 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7799 (t80) REVERT: A 198 ASP cc_start: 0.7325 (m-30) cc_final: 0.6842 (m-30) REVERT: A 211 ARG cc_start: 0.7628 (mtm-85) cc_final: 0.7374 (mtm-85) REVERT: B 219 ARG cc_start: 0.8472 (mtp85) cc_final: 0.8216 (mtp85) REVERT: B 269 ILE cc_start: 0.8768 (mt) cc_final: 0.8501 (mm) REVERT: B 314 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7671 (ttm170) REVERT: N 83 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.6597 (mtm) REVERT: R 192 PHE cc_start: 0.7520 (t80) cc_final: 0.6885 (t80) REVERT: R 243 ILE cc_start: 0.6234 (OUTLIER) cc_final: 0.6023 (mm) REVERT: R 252 PHE cc_start: 0.4405 (OUTLIER) cc_final: 0.3158 (m-80) REVERT: R 262 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6504 (tp30) REVERT: R 271 MET cc_start: 0.7128 (mtp) cc_final: 0.6865 (mtp) outliers start: 44 outliers final: 18 residues processed: 257 average time/residue: 1.2531 time to fit residues: 342.5626 Evaluate side-chains 244 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 243 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 81 optimal weight: 0.9990 chunk 73 optimal weight: 0.0870 chunk 91 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 134 ASN A 149 GLN A 217 HIS A 226 ASN A 242 ASN B 17 GLN B 75 GLN B 110 ASN B 125 ASN B 259 GLN R 89 ASN ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 151 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.161124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133267 restraints weight = 11890.012| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.92 r_work: 0.3560 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8417 Z= 0.148 Angle : 0.560 9.236 11408 Z= 0.295 Chirality : 0.042 0.139 1293 Planarity : 0.004 0.056 1440 Dihedral : 5.281 75.925 1150 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.13 % Favored : 96.77 % Rotamer: Outliers : 4.89 % Allowed : 20.67 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1021 helix: 2.13 (0.25), residues: 413 sheet: -0.14 (0.32), residues: 234 loop : -1.08 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 120 HIS 0.003 0.001 HIS A 212 PHE 0.012 0.002 PHE R 88 TYR 0.023 0.001 TYR A 194 ARG 0.008 0.001 ARG N 67 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 443) hydrogen bonds : angle 4.19734 ( 1278) SS BOND : bond 0.00546 ( 3) SS BOND : angle 2.58269 ( 6) covalent geometry : bond 0.00324 ( 8414) covalent geometry : angle 0.55736 (11402) *********************** 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 268 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7260 (mt-10) REVERT: A 139 THR cc_start: 0.8378 (p) cc_final: 0.7998 (t) REVERT: A 145 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7850 (t80) REVERT: A 198 ASP cc_start: 0.7114 (m-30) cc_final: 0.6737 (m-30) REVERT: B 219 ARG cc_start: 0.8451 (mtp85) cc_final: 0.8226 (mtp85) REVERT: B 228 ASP cc_start: 0.7829 (p0) cc_final: 0.7555 (p0) REVERT: B 264 TYR cc_start: 0.8622 (m-80) cc_final: 0.8351 (m-80) REVERT: B 314 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7696 (ttm170) REVERT: N 34 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7867 (mtm) REVERT: R 22 ILE cc_start: 0.6942 (mm) cc_final: 0.6659 (mm) REVERT: R 61 TRP cc_start: 0.5490 (m100) cc_final: 0.5227 (m100) REVERT: R 122 ILE cc_start: 0.6552 (OUTLIER) cc_final: 0.6304 (mp) REVERT: R 241 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6390 (mp) REVERT: R 244 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.7032 (mm) REVERT: R 252 PHE cc_start: 0.4241 (OUTLIER) cc_final: 0.3169 (m-80) REVERT: R 262 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6489 (tp30) REVERT: R 271 MET cc_start: 0.7171 (mtp) cc_final: 0.6937 (mtp) outliers start: 44 outliers final: 16 residues processed: 247 average time/residue: 1.2568 time to fit residues: 329.3581 Evaluate side-chains 238 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 49 ASP 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 79 LEU Chi-restraints excluded: chain B residue 93 ILE 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 84 THR 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 93 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 B 17 GLN B 88 ASN B 110 ASN B 125 ASN R 60 GLN ** R 112 HIS ** 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 = 0.4051 r_free = 0.4051 target = 0.159644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.131863 restraints weight = 11690.966| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.89 r_work: 0.3537 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8417 Z= 0.198 Angle : 0.576 9.983 11408 Z= 0.303 Chirality : 0.043 0.153 1293 Planarity : 0.004 0.055 1440 Dihedral : 4.794 68.693 1146 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.13 % Favored : 96.77 % Rotamer: Outliers : 4.33 % Allowed : 22.67 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.26), residues: 1021 helix: 2.08 (0.24), residues: 412 sheet: -0.45 (0.32), residues: 236 loop : -1.10 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 120 HIS 0.002 0.001 HIS B 225 PHE 0.031 0.002 PHE R 192 TYR 0.027 0.002 TYR A 194 ARG 0.006 0.001 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.04274 ( 443) hydrogen bonds : angle 4.19037 ( 1278) SS BOND : bond 0.00650 ( 3) SS BOND : angle 2.40336 ( 6) covalent geometry : bond 0.00438 ( 8414) covalent geometry : angle 0.57313 (11402) *********************** 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 264 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7285 (mt-10) REVERT: A 123 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7290 (mt-10) REVERT: A 139 THR cc_start: 0.8458 (p) cc_final: 0.8076 (t) REVERT: A 145 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7848 (t80) REVERT: A 198 ASP cc_start: 0.7208 (m-30) cc_final: 0.6869 (m-30) REVERT: B 219 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8183 (mtp85) REVERT: B 228 ASP cc_start: 0.7776 (p0) cc_final: 0.7556 (p0) REVERT: B 314 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7757 (ttm170) REVERT: N 34 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7903 (mtm) REVERT: R 61 TRP cc_start: 0.5560 (m100) cc_final: 0.5349 (m100) REVERT: R 90 ILE cc_start: 0.6497 (mm) cc_final: 0.6240 (mm) REVERT: R 241 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6593 (mp) REVERT: R 243 ILE cc_start: 0.6107 (mm) cc_final: 0.5217 (mt) REVERT: R 244 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7085 (mm) REVERT: R 252 PHE cc_start: 0.4474 (OUTLIER) cc_final: 0.3649 (m-80) REVERT: R 262 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6608 (tp30) REVERT: R 268 PHE cc_start: 0.6189 (m-80) cc_final: 0.5375 (t80) REVERT: R 271 MET cc_start: 0.7222 (mtp) cc_final: 0.6960 (mtp) outliers start: 39 outliers final: 18 residues processed: 248 average time/residue: 1.3940 time to fit residues: 366.6965 Evaluate side-chains 243 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 49 ASP 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 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 38 MET Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 43 LYS 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 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 25 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN A 226 ASN B 17 GLN B 88 ASN B 110 ASN B 125 ASN B 220 GLN ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.159560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.131835 restraints weight = 11591.949| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.89 r_work: 0.3538 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8417 Z= 0.196 Angle : 0.581 10.830 11408 Z= 0.306 Chirality : 0.043 0.160 1293 Planarity : 0.004 0.056 1440 Dihedral : 4.743 61.829 1146 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.33 % Favored : 96.57 % Rotamer: Outliers : 5.33 % Allowed : 22.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.26), residues: 1021 helix: 2.04 (0.24), residues: 414 sheet: -0.45 (0.32), residues: 235 loop : -1.07 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.003 0.001 HIS R 181 PHE 0.028 0.002 PHE R 192 TYR 0.027 0.002 TYR A 194 ARG 0.008 0.001 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 443) hydrogen bonds : angle 4.17581 ( 1278) SS BOND : bond 0.00496 ( 3) SS BOND : angle 2.00615 ( 6) covalent geometry : bond 0.00434 ( 8414) covalent geometry : angle 0.57930 (11402) *********************** 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 269 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 221 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7254 (mt-10) REVERT: A 139 THR cc_start: 0.8442 (p) cc_final: 0.8057 (t) REVERT: A 145 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7885 (t80) REVERT: A 198 ASP cc_start: 0.7233 (m-30) cc_final: 0.6855 (m-30) REVERT: B 219 ARG cc_start: 0.8465 (mtp85) cc_final: 0.8177 (mtp85) REVERT: B 314 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7720 (ttm170) REVERT: N 34 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7880 (mtm) REVERT: N 36 TRP cc_start: 0.8790 (m100) cc_final: 0.8399 (m100) REVERT: R 61 TRP cc_start: 0.5725 (m100) cc_final: 0.5461 (m100) REVERT: R 90 ILE cc_start: 0.6508 (mm) cc_final: 0.6238 (mm) REVERT: R 121 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6672 (mmt-90) REVERT: R 243 ILE cc_start: 0.6223 (mm) cc_final: 0.5369 (mt) REVERT: R 252 PHE cc_start: 0.4385 (OUTLIER) cc_final: 0.3627 (m-80) REVERT: R 262 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6482 (tp30) REVERT: R 271 MET cc_start: 0.7283 (mtp) cc_final: 0.7023 (mtp) outliers start: 48 outliers final: 24 residues processed: 244 average time/residue: 1.3267 time to fit residues: 343.4268 Evaluate side-chains 248 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 49 ASP 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 156 VAL 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 318 LEU 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 57 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 121 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.0670 chunk 55 optimal weight: 0.7980 chunk 73 optimal weight: 0.0070 chunk 80 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 66 optimal weight: 0.0070 chunk 97 optimal weight: 0.9980 overall best weight: 0.3354 ------------------------------------------------------------------------------- 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 126 ASN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN A 226 ASN B 17 GLN B 88 ASN B 110 ASN B 125 ASN R 112 HIS R 181 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.161040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133464 restraints weight = 11666.191| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.91 r_work: 0.3564 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8417 Z= 0.129 Angle : 0.563 14.917 11408 Z= 0.293 Chirality : 0.042 0.160 1293 Planarity : 0.004 0.055 1440 Dihedral : 4.531 54.713 1146 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.04 % Favored : 96.87 % Rotamer: Outliers : 4.67 % Allowed : 23.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1021 helix: 2.30 (0.25), residues: 411 sheet: -0.48 (0.32), residues: 234 loop : -1.03 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.003 0.001 HIS R 181 PHE 0.027 0.002 PHE R 192 TYR 0.023 0.001 TYR R 266 ARG 0.009 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 443) hydrogen bonds : angle 3.99615 ( 1278) SS BOND : bond 0.00737 ( 3) SS BOND : angle 1.70655 ( 6) covalent geometry : bond 0.00276 ( 8414) covalent geometry : angle 0.56228 (11402) *********************** 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 262 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 220 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7346 (mm-30) REVERT: A 123 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7221 (mt-10) REVERT: A 139 THR cc_start: 0.8415 (p) cc_final: 0.8033 (t) REVERT: A 145 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.7910 (t80) REVERT: A 198 ASP cc_start: 0.7142 (m-30) cc_final: 0.6735 (m-30) REVERT: B 219 ARG cc_start: 0.8484 (mtp85) cc_final: 0.8156 (mtp85) REVERT: B 264 TYR cc_start: 0.8605 (m-80) cc_final: 0.8405 (m-80) REVERT: B 314 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7673 (ttm170) REVERT: N 34 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7798 (mtm) REVERT: N 36 TRP cc_start: 0.8703 (m100) cc_final: 0.8364 (m100) REVERT: R 61 TRP cc_start: 0.5577 (m100) cc_final: 0.5375 (m100) REVERT: R 90 ILE cc_start: 0.6504 (mm) cc_final: 0.6226 (mm) REVERT: R 219 MET cc_start: 0.5471 (mmm) cc_final: 0.5214 (mmm) REVERT: R 243 ILE cc_start: 0.6223 (mm) cc_final: 0.5318 (mt) REVERT: R 271 MET cc_start: 0.7238 (mtp) cc_final: 0.6946 (mtp) outliers start: 42 outliers final: 20 residues processed: 242 average time/residue: 1.2059 time to fit residues: 309.4489 Evaluate side-chains 242 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 219 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 49 ASP 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 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 138 GLU 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 57 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 126 ASN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN A 226 ASN B 88 ASN B 110 ASN B 125 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.159325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.131579 restraints weight = 11571.891| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.90 r_work: 0.3538 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8417 Z= 0.199 Angle : 0.597 10.494 11408 Z= 0.311 Chirality : 0.043 0.173 1293 Planarity : 0.004 0.055 1440 Dihedral : 4.574 44.016 1146 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.62 % Favored : 96.28 % Rotamer: Outliers : 4.67 % Allowed : 24.33 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.26), residues: 1021 helix: 2.16 (0.25), residues: 411 sheet: -0.50 (0.32), residues: 236 loop : -1.02 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 120 HIS 0.003 0.001 HIS R 181 PHE 0.026 0.002 PHE R 192 TYR 0.026 0.002 TYR A 194 ARG 0.009 0.001 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 443) hydrogen bonds : angle 4.06484 ( 1278) SS BOND : bond 0.00660 ( 3) SS BOND : angle 1.69008 ( 6) covalent geometry : bond 0.00441 ( 8414) covalent geometry : angle 0.59583 (11402) *********************** 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 268 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 226 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7387 (mm-30) REVERT: A 123 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7282 (mt-10) REVERT: A 139 THR cc_start: 0.8452 (p) cc_final: 0.8056 (t) REVERT: A 145 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7865 (t80) REVERT: A 198 ASP cc_start: 0.7194 (m-30) cc_final: 0.6831 (m-30) REVERT: A 202 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7632 (ttp-110) REVERT: B 219 ARG cc_start: 0.8467 (mtp85) cc_final: 0.8138 (mtp85) REVERT: B 228 ASP cc_start: 0.7728 (p0) cc_final: 0.7160 (p0) REVERT: B 314 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7717 (ttm170) REVERT: N 34 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7888 (mtm) REVERT: N 36 TRP cc_start: 0.8722 (m100) cc_final: 0.8346 (m100) REVERT: N 83 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.6208 (mmm) REVERT: R 61 TRP cc_start: 0.5544 (m100) cc_final: 0.5342 (m100) REVERT: R 193 LEU cc_start: 0.7683 (tp) cc_final: 0.7456 (tm) REVERT: R 219 MET cc_start: 0.5506 (mmm) cc_final: 0.5166 (mmm) REVERT: R 240 PHE cc_start: 0.6964 (t80) cc_final: 0.6650 (t80) REVERT: R 241 LEU cc_start: 0.6940 (pp) cc_final: 0.6367 (mm) REVERT: R 243 ILE cc_start: 0.6319 (mm) cc_final: 0.6101 (mm) REVERT: R 262 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6498 (tp30) REVERT: R 271 MET cc_start: 0.7240 (mtp) cc_final: 0.6936 (mtp) outliers start: 42 outliers final: 19 residues processed: 249 average time/residue: 1.1923 time to fit residues: 314.4856 Evaluate side-chains 246 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU 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 138 ARG 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 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 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 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 84 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 52 optimal weight: 0.5980 chunk 28 optimal weight: 0.0970 chunk 86 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 126 ASN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN A 226 ASN B 17 GLN B 110 ASN B 125 ASN ** B 340 ASN ** 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 = 0.4056 r_free = 0.4056 target = 0.159963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.132403 restraints weight = 11744.246| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.91 r_work: 0.3553 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8417 Z= 0.157 Angle : 0.583 10.474 11408 Z= 0.305 Chirality : 0.042 0.169 1293 Planarity : 0.004 0.055 1440 Dihedral : 4.482 37.697 1146 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.04 % Favored : 96.87 % Rotamer: Outliers : 3.67 % Allowed : 26.22 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1021 helix: 2.23 (0.25), residues: 411 sheet: -0.55 (0.32), residues: 234 loop : -1.00 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 261 HIS 0.003 0.001 HIS A 212 PHE 0.032 0.002 PHE R 189 TYR 0.024 0.002 TYR R 266 ARG 0.009 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 443) hydrogen bonds : angle 3.99910 ( 1278) SS BOND : bond 0.00520 ( 3) SS BOND : angle 1.33429 ( 6) covalent geometry : bond 0.00346 ( 8414) covalent geometry : angle 0.58275 (11402) *********************** 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 245 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7362 (mm-30) REVERT: A 123 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7257 (mt-10) REVERT: A 139 THR cc_start: 0.8420 (p) cc_final: 0.8043 (t) REVERT: A 145 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7903 (t80) REVERT: A 198 ASP cc_start: 0.7176 (m-30) cc_final: 0.6796 (m-30) REVERT: A 202 ARG cc_start: 0.8051 (ttp80) cc_final: 0.7803 (ttp-110) REVERT: B 219 ARG cc_start: 0.8496 (mtp85) cc_final: 0.8150 (mtp85) REVERT: B 264 TYR cc_start: 0.8597 (m-80) cc_final: 0.8364 (m-80) REVERT: B 314 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7679 (ttm170) REVERT: N 34 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7819 (mtm) REVERT: N 36 TRP cc_start: 0.8661 (m100) cc_final: 0.8375 (m100) REVERT: N 83 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.6211 (mmm) REVERT: R 193 LEU cc_start: 0.7607 (tp) cc_final: 0.7366 (tm) REVERT: R 219 MET cc_start: 0.5511 (mmm) cc_final: 0.5133 (mmm) REVERT: R 240 PHE cc_start: 0.6970 (t80) cc_final: 0.6724 (t80) REVERT: R 241 LEU cc_start: 0.6923 (pp) cc_final: 0.6408 (mt) REVERT: R 243 ILE cc_start: 0.6261 (mm) cc_final: 0.6015 (mm) REVERT: R 262 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6521 (tp30) REVERT: R 271 MET cc_start: 0.7155 (mtp) cc_final: 0.6832 (mtp) outliers start: 33 outliers final: 19 residues processed: 228 average time/residue: 1.3075 time to fit residues: 315.4403 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 : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU 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 238 ILE Chi-restraints excluded: chain A residue 244 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 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 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 84 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 61 optimal weight: 0.0670 chunk 73 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN A 217 HIS B 110 ASN B 125 ASN B 230 ASN B 340 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.160430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.132785 restraints weight = 11849.875| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.93 r_work: 0.3554 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2596 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= 0.146 Angle : 0.593 11.630 11408 Z= 0.306 Chirality : 0.042 0.170 1293 Planarity : 0.004 0.055 1440 Dihedral : 4.369 29.601 1146 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.38 % Rotamer: Outliers : 3.22 % Allowed : 26.78 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1021 helix: 2.25 (0.24), residues: 412 sheet: -0.45 (0.32), residues: 238 loop : -0.94 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP R 261 HIS 0.003 0.001 HIS A 212 PHE 0.034 0.002 PHE R 189 TYR 0.022 0.001 TYR R 266 ARG 0.010 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 443) hydrogen bonds : angle 3.96326 ( 1278) SS BOND : bond 0.00452 ( 3) SS BOND : angle 1.25881 ( 6) covalent geometry : bond 0.00320 ( 8414) covalent geometry : angle 0.59212 (11402) *********************** 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 233 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7342 (mm-30) REVERT: A 120 ARG cc_start: 0.8360 (mmm-85) cc_final: 0.8054 (mmm-85) REVERT: A 123 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7280 (mt-10) REVERT: A 139 THR cc_start: 0.8430 (p) cc_final: 0.8056 (t) REVERT: A 145 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7861 (t80) REVERT: A 198 ASP cc_start: 0.7161 (m-30) cc_final: 0.6761 (m-30) REVERT: A 202 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7695 (ttp-110) REVERT: B 10 GLU cc_start: 0.7938 (tp30) cc_final: 0.7727 (tp30) REVERT: B 219 ARG cc_start: 0.8527 (mtp85) cc_final: 0.8206 (mtp85) REVERT: B 314 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7677 (ttm170) REVERT: N 34 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7848 (mtm) REVERT: N 36 TRP cc_start: 0.8645 (m100) cc_final: 0.8378 (m100) REVERT: R 90 ILE cc_start: 0.6515 (mm) cc_final: 0.6252 (mm) REVERT: R 219 MET cc_start: 0.5553 (mmm) cc_final: 0.5161 (mmm) REVERT: R 240 PHE cc_start: 0.6941 (t80) cc_final: 0.6736 (t80) REVERT: R 243 ILE cc_start: 0.6263 (mm) cc_final: 0.5280 (mt) REVERT: R 271 MET cc_start: 0.7114 (mtp) cc_final: 0.6767 (mtp) outliers start: 29 outliers final: 19 residues processed: 218 average time/residue: 1.3620 time to fit residues: 313.3529 Evaluate side-chains 225 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU 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 238 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 134 ARG 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 57 SER 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 260 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 14 optimal weight: 0.0670 chunk 16 optimal weight: 0.1980 chunk 82 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 55 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 overall best weight: 0.3318 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 125 ASN B 230 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.160955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.133682 restraints weight = 11693.122| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.91 r_work: 0.3572 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8417 Z= 0.130 Angle : 0.591 12.908 11408 Z= 0.303 Chirality : 0.042 0.169 1293 Planarity : 0.004 0.056 1440 Dihedral : 4.255 26.992 1146 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.13 % Favored : 96.77 % Rotamer: Outliers : 2.67 % Allowed : 27.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.26), residues: 1021 helix: 2.25 (0.24), residues: 419 sheet: -0.49 (0.32), residues: 236 loop : -0.94 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 261 HIS 0.002 0.001 HIS A 212 PHE 0.033 0.002 PHE R 189 TYR 0.022 0.001 TYR R 266 ARG 0.011 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 443) hydrogen bonds : angle 3.91074 ( 1278) SS BOND : bond 0.00407 ( 3) SS BOND : angle 1.22714 ( 6) covalent geometry : bond 0.00283 ( 8414) covalent geometry : angle 0.59034 (11402) ********************** 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 226 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7297 (mm-30) REVERT: A 120 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.8039 (mmm-85) REVERT: A 123 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7282 (mt-10) REVERT: A 139 THR cc_start: 0.8353 (p) cc_final: 0.7970 (t) REVERT: A 145 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7800 (t80) REVERT: A 198 ASP cc_start: 0.7112 (m-30) cc_final: 0.6724 (m-30) REVERT: A 202 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7730 (ttp-110) REVERT: B 10 GLU cc_start: 0.7953 (tp30) cc_final: 0.7725 (tp30) REVERT: B 219 ARG cc_start: 0.8523 (mtp85) cc_final: 0.8216 (mtp85) REVERT: B 314 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7677 (ttm170) REVERT: N 34 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7787 (mtm) REVERT: N 36 TRP cc_start: 0.8615 (m100) cc_final: 0.8382 (m100) REVERT: N 83 MET cc_start: 0.7745 (mmm) cc_final: 0.7131 (mtt) REVERT: R 219 MET cc_start: 0.5580 (mmm) cc_final: 0.5201 (mmm) REVERT: R 240 PHE cc_start: 0.6925 (t80) cc_final: 0.6568 (t80) REVERT: R 244 LEU cc_start: 0.7052 (mm) cc_final: 0.6833 (mp) REVERT: R 271 MET cc_start: 0.7066 (mtp) cc_final: 0.6769 (mtp) outliers start: 24 outliers final: 16 residues processed: 215 average time/residue: 1.2644 time to fit residues: 287.6298 Evaluate side-chains 218 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 72 ILE 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 244 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 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 N residue 91 THR Chi-restraints excluded: chain R residue 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 88 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 78 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 97 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.158932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.131430 restraints weight = 11772.564| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.90 r_work: 0.3534 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8417 Z= 0.208 Angle : 0.626 13.010 11408 Z= 0.324 Chirality : 0.044 0.182 1293 Planarity : 0.004 0.055 1440 Dihedral : 4.453 27.919 1146 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.38 % Rotamer: Outliers : 2.89 % Allowed : 27.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1021 helix: 2.18 (0.24), residues: 414 sheet: -0.44 (0.32), residues: 239 loop : -0.93 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 120 HIS 0.002 0.001 HIS B 62 PHE 0.034 0.002 PHE R 189 TYR 0.023 0.002 TYR A 194 ARG 0.010 0.001 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 443) hydrogen bonds : angle 4.04061 ( 1278) SS BOND : bond 0.00469 ( 3) SS BOND : angle 1.48259 ( 6) covalent geometry : bond 0.00464 ( 8414) covalent geometry : angle 0.62554 (11402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8125.28 seconds wall clock time: 140 minutes 51.22 seconds (8451.22 seconds total)