Starting phenix.real_space_refine on Sat Aug 23 01:17:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xqo_38583/08_2025/8xqo_38583.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xqo_38583/08_2025/8xqo_38583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xqo_38583/08_2025/8xqo_38583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xqo_38583/08_2025/8xqo_38583.map" model { file = "/net/cci-nas-00/data/ceres_data/8xqo_38583/08_2025/8xqo_38583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xqo_38583/08_2025/8xqo_38583.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 5736 2.51 5 N 1512 2.21 5 O 1651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8958 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2282 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 3, 'TRANS': 277} Chain breaks: 2 Chain: "R" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'CLR': 1, 'GOQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.73, per 1000 atoms: 0.19 Number of scatterers: 8958 At special positions: 0 Unit cell: (89.44, 119.6, 125.84, 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 59 16.00 O 1651 8.00 N 1512 7.00 C 5736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 289.8 milliseconds Enol-peptide restraints added in 1.4 microseconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 39.6% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.632A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.604A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.556A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.164A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 208 through 212 Processing helix chain 'R' and resid 3 through 37 Processing helix chain 'R' and resid 42 through 71 Processing helix chain 'R' and resid 80 through 112 Processing helix chain 'R' and resid 116 through 124 Processing helix chain 'R' and resid 125 through 137 Processing helix chain 'R' and resid 137 through 162 Processing helix chain 'R' and resid 173 through 216 Proline residue: R 190 - end of helix Processing helix chain 'R' and resid 227 through 253 Processing helix chain 'R' and resid 260 through 284 removed outlier: 4.236A pdb=" N TYR R 272 " --> pdb=" O MET R 268 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 4.229A pdb=" N SER R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.567A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.885A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.752A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.317A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.247A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.231A 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: 6.869A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.329A 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: 6.452A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.584A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.654A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.654A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.514A pdb=" N VAL S 143 " --> pdb=" O ILE S 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.757A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1383 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2845 1.34 - 1.46: 1634 1.46 - 1.57: 4582 1.57 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 9148 Sorted by residual: bond pdb=" C8 GOQ R 501 " pdb=" C9 GOQ R 501 " ideal model delta sigma weight residual 1.350 1.386 -0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" C5 GOQ R 501 " pdb=" C6 GOQ R 501 " ideal model delta sigma weight residual 1.454 1.421 0.033 2.00e-02 2.50e+03 2.67e+00 bond pdb=" C10 GOQ R 501 " pdb=" C9 GOQ R 501 " ideal model delta sigma weight residual 1.423 1.393 0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" O GOQ R 501 " pdb=" C1 GOQ R 501 " ideal model delta sigma weight residual 1.340 1.367 -0.027 2.00e-02 2.50e+03 1.89e+00 bond pdb=" CB MET R 212 " pdb=" CG MET R 212 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.75e+00 ... (remaining 9143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 12298 2.74 - 5.47: 70 5.47 - 8.21: 9 8.21 - 10.95: 1 10.95 - 13.68: 2 Bond angle restraints: 12380 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 112.96 108.57 4.39 1.00e+00 1.00e+00 1.93e+01 angle pdb=" CB MET R 212 " pdb=" CG MET R 212 " pdb=" SD MET R 212 " ideal model delta sigma weight residual 112.70 100.88 11.82 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CA LEU R 75 " pdb=" CB LEU R 75 " pdb=" CG LEU R 75 " ideal model delta sigma weight residual 116.30 129.98 -13.68 3.50e+00 8.16e-02 1.53e+01 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 127.55 -6.01 1.91e+00 2.74e-01 9.90e+00 angle pdb=" C PHE R 72 " pdb=" CA PHE R 72 " pdb=" CB PHE R 72 " ideal model delta sigma weight residual 111.15 116.02 -4.87 1.65e+00 3.67e-01 8.70e+00 ... (remaining 12375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 4732 17.58 - 35.15: 553 35.15 - 52.73: 140 52.73 - 70.31: 16 70.31 - 87.88: 5 Dihedral angle restraints: 5446 sinusoidal: 2171 harmonic: 3275 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 63.53 29.47 1 1.00e+01 1.00e-02 1.24e+01 dihedral pdb=" CB GLU A 207 " pdb=" CG GLU A 207 " pdb=" CD GLU A 207 " pdb=" OE1 GLU A 207 " ideal model delta sinusoidal sigma weight residual 0.00 -87.88 87.88 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CA GLU S 222 " pdb=" C GLU S 222 " pdb=" N TYR S 223 " pdb=" CA TYR S 223 " ideal model delta harmonic sigma weight residual -180.00 -164.18 -15.82 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 5443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1103 0.045 - 0.090: 224 0.090 - 0.135: 72 0.135 - 0.180: 7 0.180 - 0.225: 2 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CB ILE R 152 " pdb=" CA ILE R 152 " pdb=" CG1 ILE R 152 " pdb=" CG2 ILE R 152 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE R 19 " pdb=" CA ILE R 19 " pdb=" CG1 ILE R 19 " pdb=" CG2 ILE R 19 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA MET R 212 " pdb=" N MET R 212 " pdb=" C MET R 212 " pdb=" CB MET R 212 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.07e-01 ... (remaining 1405 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 72 " 0.052 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO R 73 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO R 73 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 73 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO S 107 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO S 224 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " 0.030 5.00e-02 4.00e+02 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 39 2.46 - 3.07: 6038 3.07 - 3.68: 13968 3.68 - 4.29: 20716 4.29 - 4.90: 34679 Nonbonded interactions: 75440 Sorted by model distance: nonbonded pdb=" O LEU R 75 " pdb=" OG1 THR R 78 " model vdw 1.853 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.074 3.040 nonbonded pdb=" OG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 2.137 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.197 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.242 3.040 ... (remaining 75435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.900 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 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 : 0.003 0.059 9150 Z= 0.141 Angle : 0.567 13.684 12384 Z= 0.285 Chirality : 0.041 0.225 1408 Planarity : 0.004 0.080 1540 Dihedral : 15.538 87.884 3322 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.10 % Allowed : 29.04 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.26), residues: 1114 helix: 2.52 (0.24), residues: 429 sheet: -0.24 (0.32), residues: 267 loop : -0.39 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 129 TYR 0.025 0.001 TYR S 223 PHE 0.013 0.001 PHE R 106 TRP 0.014 0.001 TRP R 98 HIS 0.003 0.001 HIS R 151 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9148) covalent geometry : angle 0.56714 (12380) SS BOND : bond 0.00103 ( 2) SS BOND : angle 0.54264 ( 4) hydrogen bonds : bond 0.15507 ( 488) hydrogen bonds : angle 5.93917 ( 1383) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 0.371 Fit side-chains REVERT: A 310 LEU cc_start: 0.8782 (mp) cc_final: 0.8556 (mt) REVERT: S 82 GLN cc_start: 0.8342 (tp40) cc_final: 0.8078 (tp-100) outliers start: 1 outliers final: 4 residues processed: 251 average time/residue: 0.4912 time to fit residues: 131.4653 Evaluate side-chains 241 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 237 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 146 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.134713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.119135 restraints weight = 13198.728| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.91 r_work: 0.3491 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9150 Z= 0.143 Angle : 0.546 14.150 12384 Z= 0.284 Chirality : 0.041 0.182 1408 Planarity : 0.004 0.071 1540 Dihedral : 5.074 53.820 1294 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.11 % Allowed : 23.62 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.26), residues: 1114 helix: 2.54 (0.24), residues: 429 sheet: -0.42 (0.30), residues: 277 loop : -0.38 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.022 0.001 TYR S 223 PHE 0.015 0.001 PHE R 72 TRP 0.018 0.001 TRP B 169 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9148) covalent geometry : angle 0.54636 (12380) SS BOND : bond 0.00286 ( 2) SS BOND : angle 0.54479 ( 4) hydrogen bonds : bond 0.04659 ( 488) hydrogen bonds : angle 4.57386 ( 1383) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 246 time to evaluate : 0.320 Fit side-chains REVERT: A 28 GLU cc_start: 0.7532 (tp30) cc_final: 0.7242 (tp30) REVERT: A 192 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8070 (mptm) REVERT: A 271 LYS cc_start: 0.8073 (ptmm) cc_final: 0.7867 (ttpt) REVERT: B 19 ARG cc_start: 0.7740 (ttm-80) cc_final: 0.7492 (ttm-80) REVERT: B 48 ARG cc_start: 0.8359 (mmm-85) cc_final: 0.7942 (mmt-90) REVERT: B 197 ARG cc_start: 0.7930 (tpp80) cc_final: 0.7416 (mmm-85) REVERT: B 325 MET cc_start: 0.8487 (mtt) cc_final: 0.8232 (mtm) REVERT: R 143 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7802 (tt) REVERT: R 148 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7557 (mm) REVERT: R 212 MET cc_start: 0.8351 (mmm) cc_final: 0.7088 (mmt) outliers start: 50 outliers final: 18 residues processed: 263 average time/residue: 0.4605 time to fit residues: 130.0688 Evaluate side-chains 258 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 237 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 148 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 0.4980 chunk 43 optimal weight: 0.0870 chunk 59 optimal weight: 0.0670 chunk 93 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.134426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.118859 restraints weight = 13228.804| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.91 r_work: 0.3494 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9150 Z= 0.130 Angle : 0.520 13.290 12384 Z= 0.269 Chirality : 0.041 0.175 1408 Planarity : 0.004 0.065 1540 Dihedral : 5.026 53.862 1290 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.21 % Allowed : 24.44 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.26), residues: 1114 helix: 2.57 (0.24), residues: 429 sheet: -0.45 (0.30), residues: 284 loop : -0.41 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.021 0.001 TYR S 223 PHE 0.015 0.001 PHE R 188 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9148) covalent geometry : angle 0.51952 (12380) SS BOND : bond 0.00273 ( 2) SS BOND : angle 0.48322 ( 4) hydrogen bonds : bond 0.04173 ( 488) hydrogen bonds : angle 4.36621 ( 1383) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 251 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8010 (m-30) cc_final: 0.7683 (m-30) REVERT: A 28 GLU cc_start: 0.7601 (tp30) cc_final: 0.7295 (tp30) REVERT: A 184 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8247 (tt) REVERT: A 192 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8056 (mptm) REVERT: A 278 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8247 (mm) REVERT: A 289 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7343 (tm-30) REVERT: A 324 THR cc_start: 0.7906 (p) cc_final: 0.7631 (t) REVERT: B 19 ARG cc_start: 0.7733 (ttm-80) cc_final: 0.7459 (ttm-80) REVERT: B 32 GLN cc_start: 0.8364 (mt0) cc_final: 0.8142 (mp10) REVERT: B 48 ARG cc_start: 0.8319 (mmm-85) cc_final: 0.7941 (mmt-90) REVERT: B 197 ARG cc_start: 0.7886 (tpp80) cc_final: 0.7418 (mmm-85) REVERT: R 143 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7826 (tt) outliers start: 51 outliers final: 25 residues processed: 273 average time/residue: 0.4983 time to fit residues: 145.7671 Evaluate side-chains 273 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 279 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 77 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.133350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.117682 restraints weight = 13466.865| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.93 r_work: 0.3471 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9150 Z= 0.177 Angle : 0.537 14.326 12384 Z= 0.278 Chirality : 0.041 0.185 1408 Planarity : 0.004 0.062 1540 Dihedral : 5.102 56.621 1290 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.42 % Allowed : 24.95 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.25), residues: 1114 helix: 2.49 (0.24), residues: 429 sheet: -0.45 (0.29), residues: 281 loop : -0.42 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.024 0.001 TYR S 223 PHE 0.015 0.002 PHE R 72 TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9148) covalent geometry : angle 0.53740 (12380) SS BOND : bond 0.00274 ( 2) SS BOND : angle 0.44460 ( 4) hydrogen bonds : bond 0.04254 ( 488) hydrogen bonds : angle 4.34537 ( 1383) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 246 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7523 (tp30) cc_final: 0.7199 (tp30) REVERT: A 184 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8356 (tt) REVERT: A 231 ASP cc_start: 0.7957 (t0) cc_final: 0.7656 (t0) REVERT: A 275 GLU cc_start: 0.7529 (tp30) cc_final: 0.7162 (tp30) REVERT: A 278 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8339 (mm) REVERT: A 289 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7366 (tm-30) REVERT: A 324 THR cc_start: 0.7945 (p) cc_final: 0.7693 (t) REVERT: B 19 ARG cc_start: 0.7762 (ttm-80) cc_final: 0.7486 (ttm-80) REVERT: B 32 GLN cc_start: 0.8314 (mt0) cc_final: 0.8058 (mp10) REVERT: B 177 THR cc_start: 0.8373 (m) cc_final: 0.8053 (p) REVERT: B 197 ARG cc_start: 0.7910 (tpp80) cc_final: 0.7413 (mmm-85) REVERT: B 234 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8526 (t80) REVERT: S 142 SER cc_start: 0.8275 (m) cc_final: 0.8041 (p) REVERT: S 234 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: R 76 PHE cc_start: 0.6603 (OUTLIER) cc_final: 0.6273 (m-80) REVERT: R 143 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7911 (tt) outliers start: 53 outliers final: 24 residues processed: 269 average time/residue: 0.5000 time to fit residues: 144.3940 Evaluate side-chains 272 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 242 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 76 PHE Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 279 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 293 ASN S 77 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.132765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.117061 restraints weight = 13278.500| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.92 r_work: 0.3464 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9150 Z= 0.197 Angle : 0.553 13.849 12384 Z= 0.284 Chirality : 0.042 0.191 1408 Planarity : 0.004 0.058 1540 Dihedral : 5.198 58.890 1290 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.73 % Allowed : 25.36 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.25), residues: 1114 helix: 2.41 (0.24), residues: 431 sheet: -0.57 (0.29), residues: 282 loop : -0.41 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.025 0.001 TYR S 223 PHE 0.014 0.002 PHE B 241 TRP 0.010 0.001 TRP R 98 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9148) covalent geometry : angle 0.55261 (12380) SS BOND : bond 0.00256 ( 2) SS BOND : angle 0.39374 ( 4) hydrogen bonds : bond 0.04303 ( 488) hydrogen bonds : angle 4.34619 ( 1383) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 242 time to evaluate : 0.409 Fit side-chains REVERT: A 28 GLU cc_start: 0.7532 (tp30) cc_final: 0.7222 (tp30) REVERT: A 184 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8354 (tt) REVERT: A 231 ASP cc_start: 0.7980 (t0) cc_final: 0.7661 (t0) REVERT: A 275 GLU cc_start: 0.7563 (tp30) cc_final: 0.7235 (tp30) REVERT: A 278 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8336 (mm) REVERT: A 289 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7377 (tm-30) REVERT: A 324 THR cc_start: 0.7923 (p) cc_final: 0.7671 (t) REVERT: B 19 ARG cc_start: 0.7770 (ttm-80) cc_final: 0.7494 (ttm-80) REVERT: B 32 GLN cc_start: 0.8323 (mt0) cc_final: 0.8051 (mp10) REVERT: B 177 THR cc_start: 0.8377 (m) cc_final: 0.8051 (p) REVERT: B 197 ARG cc_start: 0.7898 (tpp80) cc_final: 0.7432 (mmm-85) REVERT: B 217 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7779 (ppp) REVERT: S 142 SER cc_start: 0.8352 (m) cc_final: 0.8109 (p) REVERT: S 234 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6715 (mp0) REVERT: R 76 PHE cc_start: 0.6628 (OUTLIER) cc_final: 0.6310 (m-80) outliers start: 56 outliers final: 30 residues processed: 268 average time/residue: 0.5342 time to fit residues: 153.1337 Evaluate side-chains 275 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 76 PHE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 279 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 0.0980 chunk 46 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN S 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.133567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.117881 restraints weight = 13268.009| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.92 r_work: 0.3475 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9150 Z= 0.151 Angle : 0.539 13.773 12384 Z= 0.276 Chirality : 0.041 0.205 1408 Planarity : 0.004 0.061 1540 Dihedral : 5.129 58.904 1290 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.73 % Allowed : 25.97 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.26), residues: 1114 helix: 2.46 (0.24), residues: 432 sheet: -0.56 (0.29), residues: 283 loop : -0.39 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.024 0.001 TYR S 223 PHE 0.012 0.001 PHE R 76 TRP 0.011 0.001 TRP R 98 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9148) covalent geometry : angle 0.53922 (12380) SS BOND : bond 0.00278 ( 2) SS BOND : angle 0.57310 ( 4) hydrogen bonds : bond 0.04117 ( 488) hydrogen bonds : angle 4.27008 ( 1383) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 242 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7527 (tp30) cc_final: 0.7211 (tp30) REVERT: A 184 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8254 (tt) REVERT: A 231 ASP cc_start: 0.7980 (t0) cc_final: 0.7655 (t0) REVERT: A 275 GLU cc_start: 0.7574 (tp30) cc_final: 0.7299 (tp30) REVERT: A 278 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8318 (mm) REVERT: A 289 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7384 (tm-30) REVERT: A 324 THR cc_start: 0.7884 (p) cc_final: 0.7632 (t) REVERT: B 19 ARG cc_start: 0.7758 (ttm-80) cc_final: 0.7463 (ttm-80) REVERT: B 32 GLN cc_start: 0.8278 (mt0) cc_final: 0.7997 (mt0) REVERT: B 197 ARG cc_start: 0.7891 (tpp80) cc_final: 0.7433 (mmm-85) REVERT: B 217 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.7786 (ppp) REVERT: B 304 ARG cc_start: 0.8354 (ttp80) cc_final: 0.8051 (ttp-170) REVERT: C 20 LYS cc_start: 0.8472 (mmtp) cc_final: 0.8242 (mmtp) REVERT: S 142 SER cc_start: 0.8348 (m) cc_final: 0.8100 (p) REVERT: S 234 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: R 76 PHE cc_start: 0.6648 (OUTLIER) cc_final: 0.6345 (m-80) outliers start: 56 outliers final: 35 residues processed: 266 average time/residue: 0.5596 time to fit residues: 158.9968 Evaluate side-chains 279 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 76 PHE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 279 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN S 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.132697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.117049 restraints weight = 13343.226| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.93 r_work: 0.3460 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9150 Z= 0.205 Angle : 0.562 13.650 12384 Z= 0.289 Chirality : 0.043 0.190 1408 Planarity : 0.004 0.063 1540 Dihedral : 5.246 56.499 1290 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.52 % Allowed : 27.10 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.25), residues: 1114 helix: 2.35 (0.24), residues: 432 sheet: -0.58 (0.30), residues: 277 loop : -0.41 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 129 TYR 0.026 0.001 TYR S 223 PHE 0.014 0.002 PHE R 188 TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS R 151 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 9148) covalent geometry : angle 0.56245 (12380) SS BOND : bond 0.00303 ( 2) SS BOND : angle 0.46317 ( 4) hydrogen bonds : bond 0.04318 ( 488) hydrogen bonds : angle 4.31398 ( 1383) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 243 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7543 (tp30) cc_final: 0.7224 (tp30) REVERT: A 184 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8352 (tt) REVERT: A 231 ASP cc_start: 0.8005 (t0) cc_final: 0.7664 (t0) REVERT: A 275 GLU cc_start: 0.7592 (tp30) cc_final: 0.7288 (tp30) REVERT: A 278 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8345 (mm) REVERT: A 289 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7401 (tm-30) REVERT: A 324 THR cc_start: 0.7896 (p) cc_final: 0.7664 (t) REVERT: B 19 ARG cc_start: 0.7782 (ttm-80) cc_final: 0.7500 (ttm-80) REVERT: B 32 GLN cc_start: 0.8317 (mt0) cc_final: 0.7945 (mt0) REVERT: B 35 ASN cc_start: 0.8066 (t0) cc_final: 0.7778 (t0) REVERT: B 197 ARG cc_start: 0.7920 (tpp80) cc_final: 0.7461 (mmm-85) REVERT: B 217 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.7764 (ppp) REVERT: C 20 LYS cc_start: 0.8490 (mmtp) cc_final: 0.8243 (mmtp) REVERT: S 109 ASP cc_start: 0.7804 (m-30) cc_final: 0.7597 (m-30) REVERT: S 142 SER cc_start: 0.8396 (m) cc_final: 0.8152 (p) REVERT: R 76 PHE cc_start: 0.6705 (OUTLIER) cc_final: 0.6355 (m-80) outliers start: 54 outliers final: 31 residues processed: 269 average time/residue: 0.5371 time to fit residues: 154.7258 Evaluate side-chains 275 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 76 PHE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 281 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 0.0970 chunk 86 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 340 ASN S 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.133624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.117990 restraints weight = 13231.479| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.92 r_work: 0.3475 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9150 Z= 0.154 Angle : 0.551 13.512 12384 Z= 0.281 Chirality : 0.042 0.171 1408 Planarity : 0.004 0.071 1540 Dihedral : 5.174 54.123 1290 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.60 % Allowed : 27.91 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.26), residues: 1114 helix: 2.41 (0.24), residues: 433 sheet: -0.55 (0.30), residues: 276 loop : -0.36 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 129 TYR 0.024 0.001 TYR S 223 PHE 0.013 0.001 PHE A 199 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9148) covalent geometry : angle 0.55052 (12380) SS BOND : bond 0.00285 ( 2) SS BOND : angle 0.53251 ( 4) hydrogen bonds : bond 0.04075 ( 488) hydrogen bonds : angle 4.26468 ( 1383) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 241 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7604 (tp30) cc_final: 0.7276 (tp30) REVERT: A 184 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8261 (tt) REVERT: A 231 ASP cc_start: 0.7974 (t0) cc_final: 0.7628 (t0) REVERT: A 275 GLU cc_start: 0.7589 (tp30) cc_final: 0.7321 (tp30) REVERT: A 289 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7363 (tm-30) REVERT: A 324 THR cc_start: 0.7826 (p) cc_final: 0.7607 (t) REVERT: B 19 ARG cc_start: 0.7771 (ttm-80) cc_final: 0.7491 (ttm-80) REVERT: B 32 GLN cc_start: 0.8268 (mt0) cc_final: 0.7823 (mt0) REVERT: B 35 ASN cc_start: 0.8038 (t0) cc_final: 0.7684 (t0) REVERT: B 37 ILE cc_start: 0.8730 (tt) cc_final: 0.8307 (pt) REVERT: B 170 ASP cc_start: 0.7993 (t0) cc_final: 0.7726 (t0) REVERT: B 197 ARG cc_start: 0.7946 (tpp80) cc_final: 0.7469 (mmm-85) REVERT: B 217 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.7785 (ppp) REVERT: C 20 LYS cc_start: 0.8457 (mmtp) cc_final: 0.8151 (mmtp) REVERT: S 142 SER cc_start: 0.8367 (m) cc_final: 0.8138 (p) REVERT: S 234 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: R 76 PHE cc_start: 0.6687 (OUTLIER) cc_final: 0.6320 (m-80) REVERT: R 212 MET cc_start: 0.8321 (mmp) cc_final: 0.7960 (mmm) REVERT: R 260 ASN cc_start: 0.8458 (m110) cc_final: 0.8173 (m-40) outliers start: 45 outliers final: 28 residues processed: 261 average time/residue: 0.5772 time to fit residues: 160.8913 Evaluate side-chains 268 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 76 PHE Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 279 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN S 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.133636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.117962 restraints weight = 13253.024| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.92 r_work: 0.3476 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9150 Z= 0.161 Angle : 0.556 13.666 12384 Z= 0.284 Chirality : 0.041 0.168 1408 Planarity : 0.004 0.075 1540 Dihedral : 5.166 52.896 1290 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.78 % Allowed : 29.04 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.26), residues: 1114 helix: 2.36 (0.24), residues: 433 sheet: -0.56 (0.30), residues: 277 loop : -0.35 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 148 TYR 0.026 0.001 TYR S 223 PHE 0.014 0.001 PHE A 199 TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9148) covalent geometry : angle 0.55561 (12380) SS BOND : bond 0.00281 ( 2) SS BOND : angle 0.57758 ( 4) hydrogen bonds : bond 0.04100 ( 488) hydrogen bonds : angle 4.25656 ( 1383) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7544 (tp30) cc_final: 0.7216 (tp30) REVERT: A 184 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8263 (tt) REVERT: A 231 ASP cc_start: 0.7977 (t0) cc_final: 0.7637 (t0) REVERT: A 275 GLU cc_start: 0.7596 (tp30) cc_final: 0.7324 (tp30) REVERT: A 289 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7375 (tm-30) REVERT: A 324 THR cc_start: 0.7826 (p) cc_final: 0.7616 (t) REVERT: B 19 ARG cc_start: 0.7753 (ttm-80) cc_final: 0.7472 (ttm-80) REVERT: B 32 GLN cc_start: 0.8241 (mt0) cc_final: 0.7800 (mt0) REVERT: B 35 ASN cc_start: 0.8055 (t0) cc_final: 0.7703 (t0) REVERT: B 37 ILE cc_start: 0.8729 (tt) cc_final: 0.8298 (pt) REVERT: B 170 ASP cc_start: 0.7949 (t0) cc_final: 0.7702 (t0) REVERT: B 197 ARG cc_start: 0.7933 (tpp80) cc_final: 0.7460 (mmm-85) REVERT: B 217 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.7787 (ppp) REVERT: C 20 LYS cc_start: 0.8446 (mmtp) cc_final: 0.8173 (mmtp) REVERT: S 142 SER cc_start: 0.8379 (m) cc_final: 0.8153 (p) REVERT: S 234 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: R 76 PHE cc_start: 0.6706 (OUTLIER) cc_final: 0.6340 (m-80) REVERT: R 212 MET cc_start: 0.8346 (mmp) cc_final: 0.7988 (mmm) REVERT: R 260 ASN cc_start: 0.8482 (m110) cc_final: 0.8206 (m-40) outliers start: 37 outliers final: 29 residues processed: 261 average time/residue: 0.5685 time to fit residues: 158.6542 Evaluate side-chains 270 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 76 PHE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 281 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 99 optimal weight: 0.0980 chunk 73 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 340 ASN S 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.133767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.118094 restraints weight = 13234.302| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.92 r_work: 0.3478 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9150 Z= 0.158 Angle : 0.559 13.530 12384 Z= 0.285 Chirality : 0.042 0.156 1408 Planarity : 0.004 0.078 1540 Dihedral : 5.086 50.980 1290 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.78 % Allowed : 28.94 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.26), residues: 1114 helix: 2.37 (0.24), residues: 433 sheet: -0.57 (0.30), residues: 277 loop : -0.36 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.026 0.001 TYR S 223 PHE 0.013 0.001 PHE R 188 TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9148) covalent geometry : angle 0.55851 (12380) SS BOND : bond 0.00273 ( 2) SS BOND : angle 0.56948 ( 4) hydrogen bonds : bond 0.04074 ( 488) hydrogen bonds : angle 4.25228 ( 1383) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 233 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7531 (tp30) cc_final: 0.7202 (tp30) REVERT: A 184 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8262 (tt) REVERT: A 231 ASP cc_start: 0.7975 (t0) cc_final: 0.7635 (t0) REVERT: A 275 GLU cc_start: 0.7602 (tp30) cc_final: 0.7336 (tp30) REVERT: A 289 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7345 (tm-30) REVERT: A 324 THR cc_start: 0.7804 (p) cc_final: 0.7602 (t) REVERT: A 340 THR cc_start: 0.8303 (m) cc_final: 0.8027 (p) REVERT: A 345 LYS cc_start: 0.8351 (mptt) cc_final: 0.8127 (mptt) REVERT: B 19 ARG cc_start: 0.7763 (ttm-80) cc_final: 0.7480 (ttm-80) REVERT: B 32 GLN cc_start: 0.8249 (mt0) cc_final: 0.7810 (mt0) REVERT: B 37 ILE cc_start: 0.8727 (tt) cc_final: 0.8311 (pt) REVERT: B 170 ASP cc_start: 0.7942 (t0) cc_final: 0.7691 (t0) REVERT: B 197 ARG cc_start: 0.7942 (tpp80) cc_final: 0.7478 (mmm-85) REVERT: B 217 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7788 (ppp) REVERT: C 20 LYS cc_start: 0.8452 (mmtp) cc_final: 0.8131 (mmtp) REVERT: S 142 SER cc_start: 0.8387 (m) cc_final: 0.8152 (p) REVERT: S 234 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: R 76 PHE cc_start: 0.6699 (OUTLIER) cc_final: 0.6338 (m-80) REVERT: R 212 MET cc_start: 0.8295 (mmp) cc_final: 0.7984 (mmm) REVERT: R 260 ASN cc_start: 0.8440 (m110) cc_final: 0.8181 (m-40) outliers start: 37 outliers final: 30 residues processed: 252 average time/residue: 0.5466 time to fit residues: 147.8089 Evaluate side-chains 266 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 76 PHE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 281 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 0.4980 chunk 15 optimal weight: 0.0980 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 340 ASN S 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.134162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.118556 restraints weight = 13131.427| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.91 r_work: 0.3485 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9150 Z= 0.140 Angle : 0.575 13.541 12384 Z= 0.290 Chirality : 0.041 0.152 1408 Planarity : 0.004 0.079 1540 Dihedral : 5.033 49.443 1290 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.68 % Allowed : 29.65 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.26), residues: 1114 helix: 2.41 (0.24), residues: 431 sheet: -0.52 (0.30), residues: 277 loop : -0.37 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.024 0.001 TYR S 223 PHE 0.015 0.001 PHE R 72 TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS R 276 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9148) covalent geometry : angle 0.57497 (12380) SS BOND : bond 0.00276 ( 2) SS BOND : angle 0.63206 ( 4) hydrogen bonds : bond 0.04032 ( 488) hydrogen bonds : angle 4.26482 ( 1383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3982.77 seconds wall clock time: 68 minutes 48.13 seconds (4128.13 seconds total)