Starting phenix.real_space_refine on Sun May 11 15:41:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kpd_62484/05_2025/9kpd_62484.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kpd_62484/05_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_62484/05_2025/9kpd_62484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kpd_62484/05_2025/9kpd_62484.map" model { file = "/net/cci-nas-00/data/ceres_data/9kpd_62484/05_2025/9kpd_62484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kpd_62484/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.09, per 1000 atoms: 0.62 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: 2.30 Conformation dependent library (CDL) restraints added in 974.5 milliseconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 10 sheets defined 42.6% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 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: 2.31 Time building geometry restraints manager: 2.57 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.350 Find NCS groups from input model: 0.080 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.130 ------------------------------------------------------------------------------- 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 : 0.855 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: 1.2852 time to fit residues: 317.1570 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 : 0.896 ------------------------------------------------------------------------------- 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 = 0.160389 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 = 11678.634| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.90 r_work: 0.3550 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 10.55 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 4.59032 ( 1278) SS BOND : bond 0.00746 ( 3) SS BOND : angle 4.50107 ( 6) covalent geometry : bond 0.00423 ( 8414) covalent geometry : angle 0.61998 (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 : 0.987 Fit side-chains revert: symmetry clash REVERT: A 139 THR cc_start: 0.8393 (p) cc_final: 0.8026 (t) REVERT: A 145 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7798 (t80) REVERT: A 198 ASP cc_start: 0.7324 (m-30) cc_final: 0.6840 (m-30) REVERT: A 211 ARG cc_start: 0.7623 (mtm-85) cc_final: 0.7369 (mtm-85) REVERT: B 219 ARG cc_start: 0.8470 (mtp85) cc_final: 0.8215 (mtp85) REVERT: B 269 ILE cc_start: 0.8767 (mt) cc_final: 0.8500 (mm) REVERT: B 314 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7671 (ttm170) REVERT: N 83 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.6599 (mtm) REVERT: R 192 PHE cc_start: 0.7525 (t80) cc_final: 0.6892 (t80) REVERT: R 243 ILE cc_start: 0.6248 (OUTLIER) cc_final: 0.6036 (mm) REVERT: R 252 PHE cc_start: 0.4394 (OUTLIER) cc_final: 0.3144 (m-80) REVERT: R 262 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6508 (tp30) REVERT: R 271 MET cc_start: 0.7117 (mtp) cc_final: 0.6855 (mtp) outliers start: 44 outliers final: 18 residues processed: 257 average time/residue: 1.1624 time to fit residues: 317.3074 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 : 1.010 ------------------------------------------------------------------------------- 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: 0.8980 chunk 73 optimal weight: 0.2980 chunk 91 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 88 ASN 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.160021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.131872 restraints weight = 11841.640| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.92 r_work: 0.3547 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8417 Z= 0.176 Angle : 0.582 9.736 11408 Z= 0.305 Chirality : 0.042 0.138 1293 Planarity : 0.004 0.056 1440 Dihedral : 5.364 74.822 1150 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 4.89 % Allowed : 21.00 % Favored : 74.11 % 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: 0.60 (0.26), residues: 1021 helix: 2.04 (0.24), residues: 413 sheet: -0.15 (0.32), residues: 234 loop : -1.10 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 120 HIS 0.002 0.001 HIS A 212 PHE 0.013 0.002 PHE R 192 TYR 0.026 0.002 TYR A 194 ARG 0.008 0.001 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 443) hydrogen bonds : angle 4.29446 ( 1278) SS BOND : bond 0.00635 ( 3) SS BOND : angle 2.84209 ( 6) covalent geometry : bond 0.00390 ( 8414) covalent geometry : angle 0.57836 (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 275 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 231 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7278 (mt-10) REVERT: A 139 THR cc_start: 0.8389 (p) cc_final: 0.7996 (t) REVERT: A 145 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7863 (t80) REVERT: A 198 ASP cc_start: 0.7181 (m-30) cc_final: 0.6818 (m-30) REVERT: A 211 ARG cc_start: 0.7596 (mtm-85) cc_final: 0.7309 (mtm-85) REVERT: B 219 ARG cc_start: 0.8421 (mtp85) cc_final: 0.8121 (mtp85) REVERT: B 228 ASP cc_start: 0.7814 (p0) cc_final: 0.7552 (p0) REVERT: B 246 ASP cc_start: 0.7309 (m-30) cc_final: 0.7090 (m-30) REVERT: B 314 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7711 (ttm170) REVERT: N 34 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7938 (mtm) REVERT: N 83 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.6640 (mtm) REVERT: R 22 ILE cc_start: 0.6941 (mm) cc_final: 0.6641 (mm) REVERT: R 61 TRP cc_start: 0.5591 (m100) cc_final: 0.5281 (m100) REVERT: R 192 PHE cc_start: 0.7533 (t80) cc_final: 0.7092 (t80) REVERT: R 241 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6511 (mp) REVERT: R 244 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.7046 (mm) REVERT: R 252 PHE cc_start: 0.4216 (OUTLIER) cc_final: 0.3090 (m-80) REVERT: R 262 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6437 (tp30) REVERT: R 271 MET cc_start: 0.7186 (mtp) cc_final: 0.6958 (mtp) outliers start: 44 outliers final: 19 residues processed: 253 average time/residue: 1.1792 time to fit residues: 316.3495 Evaluate side-chains 247 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 179 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 G residue 38 MET Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 83 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 93 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 R 60 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 = 0.4055 r_free = 0.4055 target = 0.159897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.132082 restraints weight = 11689.042| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.90 r_work: 0.3545 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8417 Z= 0.176 Angle : 0.565 9.627 11408 Z= 0.297 Chirality : 0.042 0.164 1293 Planarity : 0.004 0.055 1440 Dihedral : 4.776 68.191 1146 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.13 % Favored : 96.77 % Rotamer: Outliers : 4.78 % Allowed : 22.11 % Favored : 73.11 % 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: 0.54 (0.26), residues: 1021 helix: 2.09 (0.24), residues: 412 sheet: -0.40 (0.32), residues: 236 loop : -1.09 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 120 HIS 0.004 0.001 HIS R 181 PHE 0.016 0.002 PHE R 268 TYR 0.027 0.001 TYR A 194 ARG 0.006 0.001 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 443) hydrogen bonds : angle 4.18906 ( 1278) SS BOND : bond 0.00614 ( 3) SS BOND : angle 2.39226 ( 6) covalent geometry : bond 0.00388 ( 8414) covalent geometry : angle 0.56229 (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 268 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7243 (mt-10) REVERT: A 139 THR cc_start: 0.8447 (p) cc_final: 0.8070 (t) REVERT: A 145 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.7857 (t80) REVERT: A 198 ASP cc_start: 0.7189 (m-30) cc_final: 0.6840 (m-30) REVERT: B 219 ARG cc_start: 0.8457 (mtp85) cc_final: 0.8203 (mtp85) REVERT: B 228 ASP cc_start: 0.7788 (p0) cc_final: 0.7532 (p0) REVERT: B 246 ASP cc_start: 0.7293 (m-30) cc_final: 0.7085 (m-30) REVERT: B 258 ASP cc_start: 0.7853 (t0) cc_final: 0.7626 (t0) REVERT: B 314 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7729 (ttm170) REVERT: G 27 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7986 (mtp85) REVERT: N 34 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7856 (mtm) REVERT: N 36 TRP cc_start: 0.8777 (m100) cc_final: 0.8492 (m100) REVERT: R 90 ILE cc_start: 0.6478 (mm) cc_final: 0.6205 (mm) REVERT: R 241 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6591 (mp) REVERT: R 243 ILE cc_start: 0.6110 (mm) cc_final: 0.5243 (mt) REVERT: R 244 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7080 (mm) REVERT: R 252 PHE cc_start: 0.4329 (OUTLIER) cc_final: 0.3471 (m-80) REVERT: R 262 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6583 (tp30) REVERT: R 268 PHE cc_start: 0.6132 (m-80) cc_final: 0.5355 (t80) REVERT: R 271 MET cc_start: 0.7185 (mtp) cc_final: 0.6922 (mtp) outliers start: 43 outliers final: 20 residues processed: 251 average time/residue: 1.1502 time to fit residues: 306.2529 Evaluate side-chains 248 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 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 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: 0.9980 chunk 46 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 91 optimal weight: 0.0970 chunk 96 optimal weight: 0.8980 chunk 48 optimal weight: 0.1980 chunk 50 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 133 ASN A 149 GLN A 226 ASN B 17 GLN B 88 ASN B 110 ASN B 125 ASN ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.160633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.133021 restraints weight = 11635.018| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.90 r_work: 0.3555 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8417 Z= 0.146 Angle : 0.553 10.045 11408 Z= 0.292 Chirality : 0.042 0.161 1293 Planarity : 0.004 0.056 1440 Dihedral : 4.646 62.596 1146 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 4.78 % Allowed : 23.11 % Favored : 72.11 % 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: 0.63 (0.26), residues: 1021 helix: 2.17 (0.24), residues: 414 sheet: -0.43 (0.32), residues: 236 loop : -1.00 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.003 0.001 HIS R 181 PHE 0.027 0.002 PHE R 57 TYR 0.023 0.001 TYR A 194 ARG 0.008 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 443) hydrogen bonds : angle 4.08866 ( 1278) SS BOND : bond 0.00512 ( 3) SS BOND : angle 1.96502 ( 6) covalent geometry : bond 0.00318 ( 8414) covalent geometry : angle 0.55159 (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: 43 poor density : 226 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7215 (mt-10) REVERT: A 134 ASN cc_start: 0.8120 (t0) cc_final: 0.7771 (t0) REVERT: A 139 THR cc_start: 0.8454 (p) cc_final: 0.8069 (t) REVERT: A 145 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7853 (t80) REVERT: A 198 ASP cc_start: 0.7167 (m-30) cc_final: 0.6780 (m-30) REVERT: B 219 ARG cc_start: 0.8460 (mtp85) cc_final: 0.8178 (mtp85) REVERT: B 228 ASP cc_start: 0.7790 (p0) cc_final: 0.7527 (p0) REVERT: B 246 ASP cc_start: 0.7258 (m-30) cc_final: 0.7044 (m-30) REVERT: B 258 ASP cc_start: 0.7882 (t0) cc_final: 0.7579 (t0) REVERT: B 264 TYR cc_start: 0.8591 (m-80) cc_final: 0.8373 (m-80) REVERT: B 314 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7708 (ttm170) REVERT: G 27 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7951 (mtp85) REVERT: N 34 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7854 (mtm) REVERT: N 36 TRP cc_start: 0.8744 (m100) cc_final: 0.8421 (m100) REVERT: N 106 ASP cc_start: 0.6966 (OUTLIER) cc_final: 0.6749 (p0) REVERT: R 90 ILE cc_start: 0.6418 (mm) cc_final: 0.6151 (mm) REVERT: R 121 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6647 (mmt-90) REVERT: R 241 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6563 (mp) REVERT: R 243 ILE cc_start: 0.6149 (mm) cc_final: 0.5231 (mt) REVERT: R 244 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.7052 (mm) REVERT: R 252 PHE cc_start: 0.4398 (OUTLIER) cc_final: 0.3671 (m-80) REVERT: R 262 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6458 (tp30) REVERT: R 268 PHE cc_start: 0.6138 (m-80) cc_final: 0.5495 (t80) REVERT: R 271 MET cc_start: 0.7227 (mtp) cc_final: 0.6955 (mtp) outliers start: 43 outliers final: 19 residues processed: 249 average time/residue: 1.1972 time to fit residues: 316.3323 Evaluate side-chains 251 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 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 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain 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 106 ASP Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 121 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 44 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 80 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 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 29 GLN A 92 GLN A 126 ASN A 133 ASN A 149 GLN A 226 ASN B 17 GLN B 75 GLN B 88 ASN B 110 ASN B 125 ASN ** 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 = 0.4048 r_free = 0.4048 target = 0.159376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.131826 restraints weight = 11622.934| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.89 r_work: 0.3536 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2280 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= 0.195 Angle : 0.573 9.797 11408 Z= 0.302 Chirality : 0.043 0.156 1293 Planarity : 0.004 0.056 1440 Dihedral : 4.642 52.523 1146 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.62 % Favored : 96.28 % Rotamer: Outliers : 5.11 % Allowed : 23.56 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.59 (0.26), residues: 1021 helix: 2.15 (0.25), residues: 412 sheet: -0.46 (0.32), residues: 237 loop : -1.02 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 120 HIS 0.003 0.001 HIS R 181 PHE 0.029 0.002 PHE R 192 TYR 0.027 0.002 TYR A 194 ARG 0.009 0.001 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 443) hydrogen bonds : angle 4.11342 ( 1278) SS BOND : bond 0.00804 ( 3) SS BOND : angle 1.92568 ( 6) covalent geometry : bond 0.00431 ( 8414) covalent geometry : angle 0.57144 (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 274 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7376 (mm-30) REVERT: A 123 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7218 (mt-10) REVERT: A 134 ASN cc_start: 0.8200 (t0) cc_final: 0.7719 (t0) REVERT: A 139 THR cc_start: 0.8447 (p) cc_final: 0.8058 (t) REVERT: A 145 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.7892 (t80) REVERT: A 198 ASP cc_start: 0.7234 (m-30) cc_final: 0.6862 (m-30) REVERT: B 219 ARG cc_start: 0.8472 (mtp85) cc_final: 0.8188 (mtp85) REVERT: B 314 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7731 (ttm170) REVERT: G 27 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8266 (mtp85) REVERT: N 34 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7844 (mtm) REVERT: N 36 TRP cc_start: 0.8728 (m100) cc_final: 0.8420 (m100) REVERT: N 106 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6723 (p0) REVERT: R 193 LEU cc_start: 0.7688 (tp) cc_final: 0.7412 (tm) REVERT: R 219 MET cc_start: 0.5539 (mmm) cc_final: 0.5302 (mmm) REVERT: R 262 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6454 (tp30) REVERT: R 271 MET cc_start: 0.7229 (mtp) cc_final: 0.6945 (mtp) outliers start: 46 outliers final: 22 residues processed: 253 average time/residue: 1.1676 time to fit residues: 313.1433 Evaluate side-chains 253 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 131 ILE Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 106 ASP 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 Chi-restraints excluded: chain R residue 262 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 chunk 41 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 133 ASN A 149 GLN A 226 ASN B 17 GLN B 110 ASN B 125 ASN B 220 GLN B 340 ASN R 112 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.160054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.132487 restraints weight = 11578.144| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.89 r_work: 0.3550 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8417 Z= 0.164 Angle : 0.590 16.020 11408 Z= 0.306 Chirality : 0.042 0.159 1293 Planarity : 0.004 0.055 1440 Dihedral : 4.541 45.920 1146 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.04 % Favored : 96.87 % Rotamer: Outliers : 4.56 % Allowed : 25.11 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.26), residues: 1021 helix: 2.11 (0.24), residues: 412 sheet: -0.45 (0.32), residues: 236 loop : -1.01 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 120 HIS 0.002 0.001 HIS G 44 PHE 0.026 0.002 PHE R 192 TYR 0.026 0.002 TYR R 266 ARG 0.010 0.001 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 443) hydrogen bonds : angle 4.05667 ( 1278) SS BOND : bond 0.00610 ( 3) SS BOND : angle 1.74447 ( 6) covalent geometry : bond 0.00358 ( 8414) covalent geometry : angle 0.58907 (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 269 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7205 (mt-10) REVERT: A 134 ASN cc_start: 0.8147 (t0) cc_final: 0.7690 (t0) REVERT: A 139 THR cc_start: 0.8425 (p) cc_final: 0.8041 (t) REVERT: A 145 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7881 (t80) REVERT: A 198 ASP cc_start: 0.7186 (m-30) cc_final: 0.6788 (m-30) REVERT: B 219 ARG cc_start: 0.8481 (mtp85) cc_final: 0.8188 (mtp85) REVERT: B 228 ASP cc_start: 0.7804 (p0) cc_final: 0.7581 (p0) REVERT: B 264 TYR cc_start: 0.8590 (m-80) cc_final: 0.8368 (m-80) REVERT: B 314 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7710 (ttm170) REVERT: G 27 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8214 (mtp85) REVERT: N 34 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7838 (mtm) REVERT: N 36 TRP cc_start: 0.8663 (m100) cc_final: 0.8363 (m100) REVERT: N 106 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6460 (p0) REVERT: R 193 LEU cc_start: 0.7681 (tp) cc_final: 0.7430 (tm) REVERT: R 219 MET cc_start: 0.5529 (mmm) cc_final: 0.5232 (mmm) REVERT: R 271 MET cc_start: 0.7234 (mtp) cc_final: 0.6923 (mtp) outliers start: 41 outliers final: 22 residues processed: 251 average time/residue: 1.1371 time to fit residues: 302.9118 Evaluate side-chains 251 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 131 ILE Chi-restraints excluded: chain A residue 133 ASN 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 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 106 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 52 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 86 optimal weight: 0.1980 chunk 98 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 133 ASN A 149 GLN A 226 ASN B 17 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 110 ASN B 125 ASN B 220 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.159917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.132320 restraints weight = 11722.184| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.91 r_work: 0.3541 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8417 Z= 0.176 Angle : 0.591 12.228 11408 Z= 0.308 Chirality : 0.042 0.158 1293 Planarity : 0.004 0.055 1440 Dihedral : 4.518 38.831 1146 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.23 % Favored : 96.67 % Rotamer: Outliers : 4.00 % Allowed : 26.11 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.11 (0.24), residues: 412 sheet: -0.47 (0.32), residues: 237 loop : -0.98 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 120 HIS 0.002 0.001 HIS G 44 PHE 0.027 0.002 PHE R 240 TYR 0.025 0.002 TYR A 194 ARG 0.010 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 443) hydrogen bonds : angle 4.06130 ( 1278) SS BOND : bond 0.00519 ( 3) SS BOND : angle 1.61518 ( 6) covalent geometry : bond 0.00387 ( 8414) covalent geometry : angle 0.59007 (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 261 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7234 (mt-10) REVERT: A 134 ASN cc_start: 0.8259 (t0) cc_final: 0.7994 (t0) REVERT: A 139 THR cc_start: 0.8444 (p) cc_final: 0.8056 (t) REVERT: A 145 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7890 (t80) REVERT: A 198 ASP cc_start: 0.7219 (m-30) cc_final: 0.6844 (m-30) REVERT: B 219 ARG cc_start: 0.8490 (mtp85) cc_final: 0.8217 (mtp85) REVERT: B 228 ASP cc_start: 0.7804 (p0) cc_final: 0.7584 (p0) REVERT: B 258 ASP cc_start: 0.7893 (t0) cc_final: 0.7654 (t0) REVERT: B 264 TYR cc_start: 0.8608 (m-80) cc_final: 0.8386 (m-80) REVERT: G 27 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7897 (mtp85) REVERT: N 34 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7852 (mtm) REVERT: N 36 TRP cc_start: 0.8669 (m100) cc_final: 0.8331 (m100) REVERT: R 193 LEU cc_start: 0.7693 (tp) cc_final: 0.7434 (tm) REVERT: R 219 MET cc_start: 0.5601 (mmm) cc_final: 0.5243 (mmm) REVERT: R 271 MET cc_start: 0.7224 (mtp) cc_final: 0.6926 (mtp) REVERT: R 273 SER cc_start: 0.7163 (t) cc_final: 0.6347 (p) outliers start: 36 outliers final: 23 residues processed: 244 average time/residue: 1.1696 time to fit residues: 303.1551 Evaluate side-chains 249 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 133 ASN 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 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 252 PHE Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 261 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 61 optimal weight: 0.0070 chunk 73 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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 133 ASN A 149 GLN A 226 ASN B 17 GLN B 110 ASN B 125 ASN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.160409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.132990 restraints weight = 11852.973| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.91 r_work: 0.3564 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2574 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= 0.144 Angle : 0.582 11.694 11408 Z= 0.303 Chirality : 0.042 0.164 1293 Planarity : 0.004 0.055 1440 Dihedral : 4.400 32.827 1146 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.04 % Favored : 96.87 % Rotamer: Outliers : 3.78 % Allowed : 26.22 % 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: 0.67 (0.26), residues: 1021 helix: 2.15 (0.25), residues: 411 sheet: -0.38 (0.32), residues: 238 loop : -0.90 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 99 HIS 0.002 0.001 HIS A 212 PHE 0.028 0.002 PHE R 192 TYR 0.023 0.002 TYR R 266 ARG 0.010 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 443) hydrogen bonds : angle 4.02445 ( 1278) SS BOND : bond 0.00488 ( 3) SS BOND : angle 1.45682 ( 6) covalent geometry : bond 0.00310 ( 8414) covalent geometry : angle 0.58097 (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 253 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.8397 (mmm-85) cc_final: 0.8114 (mmm-85) REVERT: A 123 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7244 (mt-10) REVERT: A 139 THR cc_start: 0.8423 (p) cc_final: 0.8050 (t) REVERT: A 145 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7916 (t80) REVERT: A 198 ASP cc_start: 0.7158 (m-30) cc_final: 0.6756 (m-30) REVERT: B 219 ARG cc_start: 0.8494 (mtp85) cc_final: 0.8166 (mtp85) REVERT: B 314 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7690 (ttm170) REVERT: G 27 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8212 (mtp85) REVERT: N 34 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7825 (mtm) REVERT: N 36 TRP cc_start: 0.8618 (m100) cc_final: 0.8381 (m100) REVERT: N 51 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8313 (mt) REVERT: R 120 TRP cc_start: 0.5845 (t60) cc_final: 0.5477 (t60) REVERT: R 193 LEU cc_start: 0.7619 (tp) cc_final: 0.7358 (tm) REVERT: R 219 MET cc_start: 0.5600 (mmm) cc_final: 0.5216 (mmm) REVERT: R 243 ILE cc_start: 0.6077 (mm) cc_final: 0.5244 (tp) REVERT: R 271 MET cc_start: 0.7133 (mtp) cc_final: 0.6840 (mtp) outliers start: 34 outliers final: 20 residues processed: 240 average time/residue: 1.1948 time to fit residues: 303.8767 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 : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 133 ASN 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 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain 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 261 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 14 optimal weight: 0.5980 chunk 16 optimal weight: 0.0030 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 0.0370 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.4068 ------------------------------------------------------------------------------- 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 133 ASN A 149 GLN A 226 ASN B 17 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 125 ASN B 230 ASN B 340 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.160432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.133150 restraints weight = 11670.573| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.90 r_work: 0.3561 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8417 Z= 0.142 Angle : 0.591 12.577 11408 Z= 0.306 Chirality : 0.042 0.164 1293 Planarity : 0.004 0.056 1440 Dihedral : 4.355 26.749 1146 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.23 % Favored : 96.67 % Rotamer: Outliers : 3.56 % Allowed : 27.11 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.73 (0.26), residues: 1021 helix: 2.16 (0.25), residues: 415 sheet: -0.33 (0.32), residues: 239 loop : -0.89 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.003 0.001 HIS A 212 PHE 0.027 0.002 PHE R 192 TYR 0.022 0.001 TYR R 266 ARG 0.011 0.001 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 443) hydrogen bonds : angle 3.98708 ( 1278) SS BOND : bond 0.00448 ( 3) SS BOND : angle 1.38862 ( 6) covalent geometry : bond 0.00309 ( 8414) covalent geometry : angle 0.59045 (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 249 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7900 (ptm-80) cc_final: 0.7619 (ptm160) REVERT: A 120 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.8085 (mmm-85) REVERT: A 123 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7271 (mt-10) REVERT: A 139 THR cc_start: 0.8426 (p) cc_final: 0.8045 (t) REVERT: A 145 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.7877 (t80) REVERT: A 198 ASP cc_start: 0.7154 (m-30) cc_final: 0.6748 (m-30) REVERT: A 202 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7734 (ttp-110) REVERT: B 219 ARG cc_start: 0.8490 (mtp85) cc_final: 0.8210 (mtp85) REVERT: B 258 ASP cc_start: 0.7883 (t0) cc_final: 0.7586 (t0) REVERT: B 314 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7682 (ttm170) REVERT: G 27 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7900 (mtp85) REVERT: N 34 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7817 (mtm) REVERT: N 36 TRP cc_start: 0.8611 (m100) cc_final: 0.8361 (m100) REVERT: N 51 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8274 (mt) REVERT: R 219 MET cc_start: 0.5622 (mmm) cc_final: 0.5226 (mmm) REVERT: R 271 MET cc_start: 0.7099 (mtp) cc_final: 0.6795 (mtp) outliers start: 32 outliers final: 21 residues processed: 235 average time/residue: 1.1860 time to fit residues: 295.2570 Evaluate side-chains 242 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 228 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 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 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 252 PHE 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 88 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 78 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 122 GLN A 133 ASN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN A 217 HIS A 226 ASN B 17 GLN B 110 ASN B 125 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.159706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.132213 restraints weight = 11754.933| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.91 r_work: 0.3558 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8417 Z= 0.181 Angle : 0.618 12.484 11408 Z= 0.320 Chirality : 0.043 0.159 1293 Planarity : 0.004 0.055 1440 Dihedral : 4.406 25.125 1146 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.62 % Favored : 96.28 % Rotamer: Outliers : 3.22 % Allowed : 28.00 % Favored : 68.78 % 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: 0.60 (0.26), residues: 1021 helix: 2.05 (0.24), residues: 417 sheet: -0.47 (0.32), residues: 237 loop : -0.90 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP R 261 HIS 0.003 0.001 HIS A 217 PHE 0.032 0.002 PHE R 102 TYR 0.023 0.002 TYR A 194 ARG 0.010 0.001 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 443) hydrogen bonds : angle 4.04882 ( 1278) SS BOND : bond 0.00485 ( 3) SS BOND : angle 1.44986 ( 6) covalent geometry : bond 0.00402 ( 8414) covalent geometry : angle 0.61736 (11402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7651.48 seconds wall clock time: 132 minutes 7.60 seconds (7927.60 seconds total)