Starting phenix.real_space_refine on Thu Mar 13 13:18:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xqo_38583/03_2025/8xqo_38583.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xqo_38583/03_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_38583/03_2025/8xqo_38583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xqo_38583/03_2025/8xqo_38583.map" model { file = "/net/cci-nas-00/data/ceres_data/8xqo_38583/03_2025/8xqo_38583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xqo_38583/03_2025/8xqo_38583.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.12, per 1000 atoms: 0.57 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: 2.10 Conformation dependent library (CDL) restraints added in 962.7 milliseconds 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: 0.89 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: 2.39 Time building geometry restraints manager: 2.48 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.470 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.680 ------------------------------------------------------------------------------- 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 9148 Z= 0.209 Angle : 0.567 13.684 12380 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.014 0.001 TRP R 98 HIS 0.003 0.001 HIS R 151 PHE 0.013 0.001 PHE R 106 TYR 0.025 0.001 TYR S 223 ARG 0.007 0.000 ARG B 129 *********************** 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 : 0.894 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: 1.1426 time to fit residues: 306.8562 Evaluate side-chains 242 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 238 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 93 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3772 r_free = 0.3772 target = 0.131886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.116487 restraints weight = 13107.342| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.87 r_work: 0.3442 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9148 Z= 0.420 Angle : 0.611 13.804 12380 Z= 0.320 Chirality : 0.045 0.221 1408 Planarity : 0.005 0.079 1540 Dihedral : 5.422 59.104 1294 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.83 % Allowed : 23.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1114 helix: 2.26 (0.24), residues: 428 sheet: -0.36 (0.30), residues: 270 loop : -0.47 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.005 0.001 HIS B 91 PHE 0.018 0.002 PHE R 248 TYR 0.028 0.002 TYR S 223 ARG 0.005 0.000 ARG B 219 *********************** 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 298 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 241 time to evaluate : 0.895 Fit side-chains REVERT: A 28 GLU cc_start: 0.7505 (tp30) cc_final: 0.7210 (tp30) REVERT: B 19 ARG cc_start: 0.7722 (ttm-80) cc_final: 0.7453 (ttm-80) REVERT: B 197 ARG cc_start: 0.7953 (tpp80) cc_final: 0.7454 (mmm-85) REVERT: B 227 SER cc_start: 0.8737 (m) cc_final: 0.8278 (t) REVERT: B 233 CYS cc_start: 0.8393 (t) cc_final: 0.8178 (p) REVERT: S 142 SER cc_start: 0.8335 (m) cc_final: 0.8125 (p) outliers start: 57 outliers final: 26 residues processed: 266 average time/residue: 1.3906 time to fit residues: 396.4406 Evaluate side-chains 254 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 192 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 SER 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 32 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 THR 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 83 MET 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 207 LEU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 279 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 3.9990 chunk 61 optimal weight: 0.0270 chunk 97 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 10 optimal weight: 0.0570 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 chunk 78 optimal weight: 0.0170 chunk 96 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 overall best weight: 0.2594 ------------------------------------------------------------------------------- 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** S 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.134934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.119224 restraints weight = 13297.575| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.93 r_work: 0.3484 rms_B_bonded: 2.44 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: 0.7727 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9148 Z= 0.162 Angle : 0.523 13.987 12380 Z= 0.270 Chirality : 0.040 0.173 1408 Planarity : 0.004 0.066 1540 Dihedral : 5.042 56.477 1288 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.60 % Allowed : 25.15 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1114 helix: 2.52 (0.25), residues: 429 sheet: -0.48 (0.30), residues: 280 loop : -0.40 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 98 HIS 0.002 0.001 HIS B 311 PHE 0.015 0.001 PHE R 82 TYR 0.022 0.001 TYR S 223 ARG 0.006 0.000 ARG B 129 *********************** 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 293 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 248 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8003 (m-30) cc_final: 0.7675 (m-30) REVERT: A 28 GLU cc_start: 0.7571 (tp30) cc_final: 0.7253 (tp30) REVERT: A 184 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8263 (tt) REVERT: A 289 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 324 THR cc_start: 0.7871 (p) cc_final: 0.7593 (t) REVERT: B 19 ARG cc_start: 0.7705 (ttm-80) cc_final: 0.7424 (ttm-80) REVERT: B 22 ARG cc_start: 0.8527 (mtt180) cc_final: 0.8249 (mtt180) REVERT: B 35 ASN cc_start: 0.8098 (t0) cc_final: 0.7827 (t0) REVERT: B 37 ILE cc_start: 0.8752 (tt) cc_final: 0.8316 (pt) REVERT: B 68 ARG cc_start: 0.8784 (ttt-90) cc_final: 0.8236 (mtp180) REVERT: B 227 SER cc_start: 0.8724 (m) cc_final: 0.8252 (t) REVERT: B 234 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8489 (t80) REVERT: S 87 ARG cc_start: 0.8275 (ptp-110) cc_final: 0.8063 (ptp-170) outliers start: 45 outliers final: 17 residues processed: 268 average time/residue: 1.1396 time to fit residues: 325.9736 Evaluate side-chains 261 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 242 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 281 SER Chi-restraints excluded: chain A residue 310 LEU 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 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE 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 135 VAL Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain R residue 76 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN S 77 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.131730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116327 restraints weight = 13385.634| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.89 r_work: 0.3464 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9148 Z= 0.246 Angle : 0.549 16.507 12380 Z= 0.280 Chirality : 0.041 0.187 1408 Planarity : 0.004 0.062 1540 Dihedral : 5.070 57.691 1288 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.62 % Allowed : 25.15 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.25), residues: 1114 helix: 2.44 (0.24), residues: 429 sheet: -0.48 (0.29), residues: 283 loop : -0.47 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS A 213 PHE 0.014 0.001 PHE R 188 TYR 0.025 0.001 TYR S 223 ARG 0.006 0.000 ARG B 219 *********************** 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 301 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 246 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7513 (tp30) cc_final: 0.7185 (tp30) REVERT: A 184 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8258 (tt) REVERT: A 192 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8141 (mptm) REVERT: A 231 ASP cc_start: 0.7974 (t0) cc_final: 0.7662 (t0) REVERT: A 271 LYS cc_start: 0.8285 (ttpt) cc_final: 0.8078 (ttpt) REVERT: A 275 GLU cc_start: 0.7613 (tp30) cc_final: 0.7239 (tp30) REVERT: A 289 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7349 (tm-30) REVERT: A 324 THR cc_start: 0.7910 (p) cc_final: 0.7656 (t) REVERT: B 19 ARG cc_start: 0.7761 (ttm-80) cc_final: 0.7478 (ttm-80) REVERT: B 22 ARG cc_start: 0.8533 (mtt180) cc_final: 0.8236 (mtt180) REVERT: B 32 GLN cc_start: 0.8379 (mt0) cc_final: 0.8093 (mt0) REVERT: B 37 ILE cc_start: 0.8748 (tt) cc_final: 0.8265 (pt) REVERT: B 68 ARG cc_start: 0.8750 (ttt-90) cc_final: 0.8355 (tpp80) REVERT: B 177 THR cc_start: 0.8383 (m) cc_final: 0.8059 (p) REVERT: B 217 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.7799 (ppp) REVERT: S 87 ARG cc_start: 0.8304 (ptp-110) cc_final: 0.8059 (ptp-170) REVERT: S 142 SER cc_start: 0.8343 (m) cc_final: 0.8079 (p) REVERT: S 179 ARG cc_start: 0.8181 (mpt-90) cc_final: 0.7786 (mpp80) REVERT: S 234 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6623 (mp0) REVERT: R 76 PHE cc_start: 0.6602 (OUTLIER) cc_final: 0.6386 (m-10) REVERT: R 143 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7842 (tt) outliers start: 55 outliers final: 29 residues processed: 274 average time/residue: 1.2206 time to fit residues: 356.7603 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 : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER 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 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 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 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 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 143 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 100 optimal weight: 0.0040 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 90 optimal weight: 0.0010 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 220 GLN B 293 ASN S 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.134080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.118310 restraints weight = 13096.150| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.91 r_work: 0.3470 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9148 Z= 0.210 Angle : 0.526 14.449 12380 Z= 0.269 Chirality : 0.041 0.178 1408 Planarity : 0.004 0.057 1540 Dihedral : 5.024 59.202 1288 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.52 % Allowed : 25.26 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1114 helix: 2.51 (0.24), residues: 430 sheet: -0.51 (0.29), residues: 284 loop : -0.44 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 98 HIS 0.003 0.001 HIS A 213 PHE 0.011 0.001 PHE R 82 TYR 0.023 0.001 TYR S 223 ARG 0.005 0.000 ARG B 219 *********************** 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 297 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 243 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7587 (tp30) cc_final: 0.7264 (tp30) REVERT: A 184 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8260 (tt) REVERT: A 192 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8050 (mptm) REVERT: A 231 ASP cc_start: 0.7990 (t0) cc_final: 0.7653 (t0) REVERT: A 275 GLU cc_start: 0.7563 (tp30) cc_final: 0.7206 (tp30) REVERT: A 289 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7327 (tm-30) REVERT: A 324 THR cc_start: 0.7860 (p) cc_final: 0.7615 (t) REVERT: B 19 ARG cc_start: 0.7733 (ttm-80) cc_final: 0.7446 (ttm-80) REVERT: B 22 ARG cc_start: 0.8547 (mtt180) cc_final: 0.8266 (mtt180) REVERT: B 32 GLN cc_start: 0.8344 (mt0) cc_final: 0.8123 (mt0) REVERT: B 37 ILE cc_start: 0.8741 (tt) cc_final: 0.8270 (pt) REVERT: B 68 ARG cc_start: 0.8781 (ttt-90) cc_final: 0.8404 (tpp80) REVERT: B 217 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.7807 (ppp) REVERT: B 219 ARG cc_start: 0.8349 (mmm-85) cc_final: 0.7941 (mtp85) REVERT: C 20 LYS cc_start: 0.8476 (mmtp) cc_final: 0.8263 (mmtp) REVERT: S 142 SER cc_start: 0.8285 (m) cc_final: 0.8077 (p) REVERT: S 234 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: R 76 PHE cc_start: 0.6632 (OUTLIER) cc_final: 0.6304 (m-80) REVERT: R 105 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8183 (m) REVERT: R 143 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7907 (tt) outliers start: 54 outliers final: 30 residues processed: 268 average time/residue: 1.1700 time to fit residues: 335.9798 Evaluate side-chains 273 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 35 LYS 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 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 281 SER Chi-restraints excluded: chain A residue 310 LEU 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 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 115 THR 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 234 GLU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 76 PHE Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 179 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.0000 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 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 = 0.133568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.117824 restraints weight = 13118.224| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.92 r_work: 0.3463 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9148 Z= 0.249 Angle : 0.541 14.297 12380 Z= 0.277 Chirality : 0.041 0.203 1408 Planarity : 0.004 0.061 1540 Dihedral : 5.049 57.578 1288 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.83 % Allowed : 26.18 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1114 helix: 2.44 (0.24), residues: 432 sheet: -0.49 (0.29), residues: 282 loop : -0.45 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS A 213 PHE 0.012 0.001 PHE B 241 TYR 0.024 0.001 TYR S 223 ARG 0.004 0.000 ARG B 219 *********************** 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 294 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 237 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7594 (tp30) cc_final: 0.7277 (tp30) REVERT: A 184 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8260 (tt) REVERT: A 192 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8082 (mptm) REVERT: A 231 ASP cc_start: 0.7968 (t0) cc_final: 0.7605 (t0) REVERT: A 275 GLU cc_start: 0.7586 (tp30) cc_final: 0.7279 (tp30) REVERT: A 289 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7353 (tm-30) REVERT: A 324 THR cc_start: 0.7848 (p) cc_final: 0.7622 (t) REVERT: B 19 ARG cc_start: 0.7738 (ttm-80) cc_final: 0.7452 (ttm-80) REVERT: B 22 ARG cc_start: 0.8563 (mtt180) cc_final: 0.8289 (mtt180) REVERT: B 32 GLN cc_start: 0.8364 (mt0) cc_final: 0.8068 (mt0) REVERT: B 35 ASN cc_start: 0.8054 (t0) cc_final: 0.7779 (t0) REVERT: B 37 ILE cc_start: 0.8751 (tt) cc_final: 0.8270 (pt) REVERT: B 68 ARG cc_start: 0.8805 (ttt-90) cc_final: 0.8430 (tpp80) REVERT: B 217 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.7813 (ppp) REVERT: B 219 ARG cc_start: 0.8364 (mmm-85) cc_final: 0.7957 (mtp85) REVERT: C 20 LYS cc_start: 0.8483 (mmtp) cc_final: 0.8276 (mmtp) REVERT: S 142 SER cc_start: 0.8355 (m) cc_final: 0.8109 (p) REVERT: S 234 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6691 (mp0) REVERT: R 76 PHE cc_start: 0.6672 (OUTLIER) cc_final: 0.6340 (m-80) REVERT: R 105 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8218 (m) REVERT: R 143 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7931 (tt) outliers start: 57 outliers final: 32 residues processed: 267 average time/residue: 1.2321 time to fit residues: 352.2145 Evaluate side-chains 280 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 192 LYS 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 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 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 11 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 115 THR 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 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 78 THR Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 179 ILE 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 103 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 220 GLN B 340 ASN S 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.133101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.117510 restraints weight = 13203.681| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.90 r_work: 0.3458 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9148 Z= 0.275 Angle : 0.554 14.868 12380 Z= 0.284 Chirality : 0.042 0.183 1408 Planarity : 0.004 0.064 1540 Dihedral : 5.112 54.873 1288 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.52 % Allowed : 26.89 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.25), residues: 1114 helix: 2.39 (0.24), residues: 431 sheet: -0.57 (0.29), residues: 280 loop : -0.45 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS A 213 PHE 0.013 0.002 PHE B 241 TYR 0.025 0.001 TYR S 223 ARG 0.004 0.000 ARG S 98 *********************** 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 298 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 244 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7533 (tp30) cc_final: 0.7216 (tp30) REVERT: A 184 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8256 (tt) REVERT: A 192 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8119 (mptm) REVERT: A 231 ASP cc_start: 0.7966 (t0) cc_final: 0.7600 (t0) REVERT: A 275 GLU cc_start: 0.7626 (tp30) cc_final: 0.7338 (tp30) REVERT: A 289 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7363 (tm-30) REVERT: A 317 LYS cc_start: 0.8065 (ptmt) cc_final: 0.7859 (ptmt) REVERT: A 324 THR cc_start: 0.7853 (p) cc_final: 0.7635 (t) REVERT: B 19 ARG cc_start: 0.7736 (ttm-80) cc_final: 0.7457 (ttm-80) REVERT: B 22 ARG cc_start: 0.8562 (mtt180) cc_final: 0.8282 (mtt180) REVERT: B 32 GLN cc_start: 0.8366 (mt0) cc_final: 0.8000 (mp10) REVERT: B 35 ASN cc_start: 0.8038 (t0) cc_final: 0.7545 (t0) REVERT: B 37 ILE cc_start: 0.8770 (tt) cc_final: 0.8360 (pt) REVERT: B 68 ARG cc_start: 0.8818 (ttt-90) cc_final: 0.8440 (tpp80) REVERT: B 217 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.7779 (ppp) REVERT: B 219 ARG cc_start: 0.8365 (mmm-85) cc_final: 0.7909 (mtp85) REVERT: C 20 LYS cc_start: 0.8492 (mmtp) cc_final: 0.8214 (mmtp) REVERT: S 109 ASP cc_start: 0.7818 (m-30) cc_final: 0.7616 (m-30) REVERT: S 142 SER cc_start: 0.8387 (m) cc_final: 0.8153 (p) REVERT: S 179 ARG cc_start: 0.8199 (mpt-90) cc_final: 0.7797 (mpp80) REVERT: S 234 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: R 76 PHE cc_start: 0.6775 (OUTLIER) cc_final: 0.6454 (m-80) outliers start: 54 outliers final: 34 residues processed: 271 average time/residue: 1.1351 time to fit residues: 327.8883 Evaluate side-chains 283 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 244 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 192 LYS 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 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 B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 115 THR 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 78 THR Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 179 ILE 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 102 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 0.0170 chunk 100 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 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 = 0.133548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.117754 restraints weight = 13405.558| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.94 r_work: 0.3462 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9148 Z= 0.239 Angle : 0.553 14.952 12380 Z= 0.280 Chirality : 0.041 0.179 1408 Planarity : 0.004 0.070 1540 Dihedral : 5.075 53.380 1288 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.11 % Allowed : 27.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.25), residues: 1114 helix: 2.46 (0.24), residues: 432 sheet: -0.56 (0.29), residues: 279 loop : -0.45 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS A 213 PHE 0.014 0.001 PHE R 106 TYR 0.025 0.001 TYR S 223 ARG 0.003 0.000 ARG B 219 *********************** 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 294 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 244 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7541 (tp30) cc_final: 0.7209 (tp30) REVERT: A 184 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8265 (tt) REVERT: A 192 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8082 (mptm) REVERT: A 231 ASP cc_start: 0.7982 (t0) cc_final: 0.7636 (t0) REVERT: A 275 GLU cc_start: 0.7629 (tp30) cc_final: 0.7334 (tp30) REVERT: A 289 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7375 (tm-30) REVERT: A 324 THR cc_start: 0.7814 (p) cc_final: 0.7593 (t) REVERT: B 19 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.7455 (ttm-80) REVERT: B 22 ARG cc_start: 0.8545 (mtt180) cc_final: 0.8273 (mtt180) REVERT: B 32 GLN cc_start: 0.8334 (mt0) cc_final: 0.7938 (mp10) REVERT: B 35 ASN cc_start: 0.8017 (t0) cc_final: 0.7663 (t0) REVERT: B 37 ILE cc_start: 0.8758 (tt) cc_final: 0.8343 (pt) REVERT: B 68 ARG cc_start: 0.8806 (ttt-90) cc_final: 0.8428 (tpp80) REVERT: B 217 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.7798 (ppp) REVERT: B 219 ARG cc_start: 0.8378 (mmm-85) cc_final: 0.7960 (mtp85) REVERT: C 20 LYS cc_start: 0.8460 (mmtp) cc_final: 0.8157 (mmtp) REVERT: S 142 SER cc_start: 0.8398 (m) cc_final: 0.8167 (p) REVERT: S 234 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: R 76 PHE cc_start: 0.6796 (OUTLIER) cc_final: 0.6461 (m-80) outliers start: 50 outliers final: 34 residues processed: 271 average time/residue: 1.2408 time to fit residues: 358.4539 Evaluate side-chains 281 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 192 LYS 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 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 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 96 CYS Chi-restraints excluded: chain S residue 115 THR 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 96 SER Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 281 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 83 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 220 GLN B 340 ASN S 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.132874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.117816 restraints weight = 13272.370| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.89 r_work: 0.3470 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9148 Z= 0.224 Angle : 0.546 14.666 12380 Z= 0.277 Chirality : 0.041 0.166 1408 Planarity : 0.004 0.076 1540 Dihedral : 5.044 51.214 1288 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.70 % Allowed : 28.22 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.25), residues: 1114 helix: 2.47 (0.24), residues: 432 sheet: -0.59 (0.29), residues: 279 loop : -0.43 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS A 213 PHE 0.014 0.001 PHE R 188 TYR 0.024 0.001 TYR S 223 ARG 0.004 0.000 ARG S 148 *********************** 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 287 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 241 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7588 (tp30) cc_final: 0.7254 (tp30) REVERT: A 184 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8261 (tt) REVERT: A 192 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8061 (mptm) REVERT: A 231 ASP cc_start: 0.7943 (t0) cc_final: 0.7594 (t0) REVERT: A 275 GLU cc_start: 0.7617 (tp30) cc_final: 0.7310 (tp30) REVERT: A 289 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7374 (tm-30) REVERT: B 19 ARG cc_start: 0.7728 (ttm-80) cc_final: 0.7430 (ttm-80) REVERT: B 32 GLN cc_start: 0.8290 (mt0) cc_final: 0.7868 (mp10) REVERT: B 37 ILE cc_start: 0.8755 (tt) cc_final: 0.8349 (pt) REVERT: B 68 ARG cc_start: 0.8804 (ttt-90) cc_final: 0.8444 (tpp80) REVERT: B 217 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.7792 (ppp) REVERT: B 219 ARG cc_start: 0.8376 (mmm-85) cc_final: 0.7958 (mtp85) REVERT: C 20 LYS cc_start: 0.8450 (mmtp) cc_final: 0.8142 (mmtp) REVERT: S 142 SER cc_start: 0.8394 (m) cc_final: 0.8169 (p) REVERT: S 234 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: R 76 PHE cc_start: 0.6765 (OUTLIER) cc_final: 0.6371 (m-80) REVERT: R 260 ASN cc_start: 0.8475 (m110) cc_final: 0.8194 (m-40) outliers start: 46 outliers final: 33 residues processed: 263 average time/residue: 1.1971 time to fit residues: 335.3445 Evaluate side-chains 265 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 192 LYS 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 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 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 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 96 SER Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 238 LEU 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 46 optimal weight: 0.7980 chunk 57 optimal weight: 0.0670 chunk 103 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 70 optimal weight: 0.0770 chunk 66 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 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 = 0.3804 r_free = 0.3804 target = 0.134245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.118606 restraints weight = 13216.888| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.90 r_work: 0.3470 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9148 Z= 0.209 Angle : 0.557 12.940 12380 Z= 0.282 Chirality : 0.041 0.156 1408 Planarity : 0.004 0.079 1540 Dihedral : 5.026 50.857 1288 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.99 % Allowed : 28.94 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1114 helix: 2.48 (0.24), residues: 432 sheet: -0.58 (0.29), residues: 279 loop : -0.41 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 98 HIS 0.004 0.001 HIS B 225 PHE 0.014 0.001 PHE R 188 TYR 0.026 0.001 TYR S 223 ARG 0.003 0.000 ARG B 219 ********************** 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 269 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 230 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7605 (tp30) cc_final: 0.7276 (tp30) REVERT: A 184 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8265 (tt) REVERT: A 192 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8068 (mptm) REVERT: A 231 ASP cc_start: 0.7925 (t0) cc_final: 0.7562 (t0) REVERT: A 275 GLU cc_start: 0.7620 (tp30) cc_final: 0.7305 (tp30) REVERT: A 289 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7368 (tm-30) REVERT: B 19 ARG cc_start: 0.7730 (ttm-80) cc_final: 0.7439 (ttm-80) REVERT: B 32 GLN cc_start: 0.8281 (mt0) cc_final: 0.7863 (mp10) REVERT: B 37 ILE cc_start: 0.8760 (tt) cc_final: 0.8359 (pt) REVERT: B 197 ARG cc_start: 0.7920 (tpp80) cc_final: 0.7504 (mmm-85) REVERT: B 217 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.7791 (ppp) REVERT: B 304 ARG cc_start: 0.8328 (ttp80) cc_final: 0.8029 (ttp-170) REVERT: C 20 LYS cc_start: 0.8448 (mmtp) cc_final: 0.8166 (mmtp) REVERT: S 142 SER cc_start: 0.8376 (m) cc_final: 0.8147 (p) REVERT: S 234 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: R 76 PHE cc_start: 0.6749 (OUTLIER) cc_final: 0.6356 (m-80) REVERT: R 260 ASN cc_start: 0.8450 (m110) cc_final: 0.8180 (m-40) outliers start: 39 outliers final: 33 residues processed: 253 average time/residue: 1.1617 time to fit residues: 314.4104 Evaluate side-chains 267 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 192 LYS 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 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 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 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 96 SER Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 238 LEU 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 71 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 220 GLN B 340 ASN S 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.133383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.117857 restraints weight = 13279.908| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.90 r_work: 0.3461 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9148 Z= 0.266 Angle : 0.562 13.245 12380 Z= 0.288 Chirality : 0.042 0.166 1408 Planarity : 0.004 0.077 1540 Dihedral : 5.146 55.405 1288 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.29 % Allowed : 28.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1114 helix: 2.41 (0.24), residues: 432 sheet: -0.65 (0.29), residues: 281 loop : -0.41 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS A 213 PHE 0.014 0.002 PHE A 199 TYR 0.027 0.001 TYR S 223 ARG 0.007 0.000 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8483.59 seconds wall clock time: 148 minutes 9.85 seconds (8889.85 seconds total)