Starting phenix.real_space_refine on Tue Feb 11 09:57:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xi8_22191/02_2025/6xi8_22191.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xi8_22191/02_2025/6xi8_22191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xi8_22191/02_2025/6xi8_22191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xi8_22191/02_2025/6xi8_22191.map" model { file = "/net/cci-nas-00/data/ceres_data/6xi8_22191/02_2025/6xi8_22191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xi8_22191/02_2025/6xi8_22191.cif" } resolution = 3.64 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= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 96 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 P 3 5.49 5 S 24 5.16 5 C 3229 2.51 5 N 836 2.21 5 O 926 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5022 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 499 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "A" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2342 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 269} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2150 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 10, 'TRANS': 273} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 101 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.71, per 1000 atoms: 0.74 Number of scatterers: 5022 At special positions: 0 Unit cell: (96.28, 85.49, 90.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 24 16.00 P 3 15.00 Al 1 13.00 F 3 9.00 O 926 8.00 N 836 7.00 C 3229 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.22 Conformation dependent library (CDL) restraints added in 602.6 milliseconds 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1232 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 51.7% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'C' and resid 284 through 287 removed outlier: 3.524A pdb=" N HIS C 287 " --> pdb=" O ASP C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 284 through 287' Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.092A pdb=" N ILE C 292 " --> pdb=" O ARG C 288 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 288 through 293' Processing helix chain 'C' and resid 297 through 309 removed outlier: 3.787A pdb=" N ALA C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 56 removed outlier: 3.988A pdb=" N ILE A 52 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 95 removed outlier: 3.774A pdb=" N VAL A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 123 removed outlier: 3.548A pdb=" N ALA A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TRP A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.770A pdb=" N ARG A 171 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 185 through 201 removed outlier: 3.915A pdb=" N TRP A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 removed outlier: 4.106A pdb=" N GLU A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.507A pdb=" N GLU A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 252' Processing helix chain 'A' and resid 262 through 271 removed outlier: 3.731A pdb=" N PHE A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'B' and resid 52 through 57 removed outlier: 3.771A pdb=" N MET B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 73 Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 94 through 106 Processing helix chain 'B' and resid 108 through 131 removed outlier: 5.504A pdb=" N LEU B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 152 removed outlier: 4.109A pdb=" N GLU B 151 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 174 removed outlier: 3.973A pdb=" N ILE B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N HIS B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE B 167 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 186 Processing helix chain 'B' and resid 198 through 206 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 223 through 229 removed outlier: 3.594A pdb=" N VAL B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 244 through 255 Processing helix chain 'B' and resid 262 through 271 Processing helix chain 'B' and resid 272 through 275 removed outlier: 3.618A pdb=" N ASP B 275 " --> pdb=" O LEU B 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 275' Processing helix chain 'B' and resid 278 through 287 removed outlier: 3.932A pdb=" N THR B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE B 287 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 345 removed outlier: 4.070A pdb=" N LEU B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP B 345 " --> pdb=" O SER B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 360 removed outlier: 4.124A pdb=" N LYS B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS B 360 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.884A pdb=" N VAL A 20 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU A 37 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 79 " --> pdb=" O ILE A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 136 167 hydrogen bonds defined for protein. 489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 823 1.31 - 1.44: 1360 1.44 - 1.56: 2900 1.56 - 1.69: 10 1.69 - 1.81: 43 Bond restraints: 5136 Sorted by residual: bond pdb=" C THR B 351 " pdb=" N GLU B 352 " ideal model delta sigma weight residual 1.333 1.554 -0.222 1.45e-02 4.76e+03 2.34e+02 bond pdb=" C1' ADP A 401 " pdb=" C2' ADP A 401 " ideal model delta sigma weight residual 1.524 1.301 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C1' ADP A 401 " pdb=" O4' ADP A 401 " ideal model delta sigma weight residual 1.426 1.629 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C GLU B 344 " pdb=" N ASP B 345 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.27e-02 6.20e+03 8.97e+01 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.342 0.148 2.00e-02 2.50e+03 5.46e+01 ... (remaining 5131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.35: 6922 7.35 - 14.69: 42 14.69 - 22.04: 3 22.04 - 29.38: 3 29.38 - 36.73: 4 Bond angle restraints: 6974 Sorted by residual: angle pdb=" O GLU B 344 " pdb=" C GLU B 344 " pdb=" N ASP B 345 " ideal model delta sigma weight residual 122.43 85.70 36.73 1.46e+00 4.69e-01 6.33e+02 angle pdb=" N ASP A 228 " pdb=" CA ASP A 228 " pdb=" C ASP A 228 " ideal model delta sigma weight residual 112.04 143.07 -31.03 1.44e+00 4.82e-01 4.64e+02 angle pdb=" N PHE B 177 " pdb=" CA PHE B 177 " pdb=" C PHE B 177 " ideal model delta sigma weight residual 111.92 128.88 -16.96 1.34e+00 5.57e-01 1.60e+02 angle pdb=" C ASP A 228 " pdb=" CA ASP A 228 " pdb=" CB ASP A 228 " ideal model delta sigma weight residual 110.56 88.32 22.24 1.83e+00 2.99e-01 1.48e+02 angle pdb=" O2P TPO A 162 " pdb=" P TPO A 162 " pdb=" O3P TPO A 162 " ideal model delta sigma weight residual 113.68 78.53 35.15 3.00e+00 1.11e-01 1.37e+02 ... (remaining 6969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.62: 3010 32.62 - 65.23: 76 65.23 - 97.85: 4 97.85 - 130.47: 0 130.47 - 163.08: 1 Dihedral angle restraints: 3091 sinusoidal: 1201 harmonic: 1890 Sorted by residual: dihedral pdb=" N PHE B 177 " pdb=" C PHE B 177 " pdb=" CA PHE B 177 " pdb=" CB PHE B 177 " ideal model delta harmonic sigma weight residual 122.80 167.25 -44.45 0 2.50e+00 1.60e-01 3.16e+02 dihedral pdb=" C PHE B 177 " pdb=" N PHE B 177 " pdb=" CA PHE B 177 " pdb=" CB PHE B 177 " ideal model delta harmonic sigma weight residual -122.60 -166.09 43.49 0 2.50e+00 1.60e-01 3.03e+02 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 136.92 163.08 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 3088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.402: 785 0.402 - 0.803: 4 0.803 - 1.205: 0 1.205 - 1.607: 0 1.607 - 2.008: 1 Chirality restraints: 790 Sorted by residual: chirality pdb=" CA PHE B 177 " pdb=" N PHE B 177 " pdb=" C PHE B 177 " pdb=" CB PHE B 177 " both_signs ideal model delta sigma weight residual False 2.51 0.50 2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" CA ASP A 228 " pdb=" N ASP A 228 " pdb=" C ASP A 228 " pdb=" CB ASP A 228 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" CA TYR B 362 " pdb=" N TYR B 362 " pdb=" C TYR B 362 " pdb=" CB TYR B 362 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 ... (remaining 787 not shown) Planarity restraints: 881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 344 " -0.123 2.00e-02 2.50e+03 1.90e-01 3.61e+02 pdb=" C GLU B 344 " 0.328 2.00e-02 2.50e+03 pdb=" O GLU B 344 " -0.112 2.00e-02 2.50e+03 pdb=" N ASP B 345 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 351 " -0.061 2.00e-02 2.50e+03 1.06e-01 1.12e+02 pdb=" C THR B 351 " 0.183 2.00e-02 2.50e+03 pdb=" O THR B 351 " -0.069 2.00e-02 2.50e+03 pdb=" N GLU B 352 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 58 " -0.039 2.00e-02 2.50e+03 4.06e-02 4.13e+01 pdb=" CG TRP B 58 " 0.105 2.00e-02 2.50e+03 pdb=" CD1 TRP B 58 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 TRP B 58 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 58 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B 58 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 58 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 58 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 58 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 58 " -0.003 2.00e-02 2.50e+03 ... (remaining 878 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.05: 1 2.05 - 2.76: 684 2.76 - 3.47: 6721 3.47 - 4.19: 11340 4.19 - 4.90: 19672 Nonbonded interactions: 38418 Sorted by model distance: nonbonded pdb=" O CYS B 364 " pdb=" CG PRO B 367 " model vdw 1.333 3.440 nonbonded pdb=" C CYS B 364 " pdb=" CG PRO B 367 " model vdw 2.113 3.670 nonbonded pdb=" O CYS B 364 " pdb=" CD PRO B 367 " model vdw 2.160 3.440 nonbonded pdb=" CG PRO A 224 " pdb=" SD MET A 273 " model vdw 2.205 3.800 nonbonded pdb=" O GLU B 344 " pdb=" N CYS B 346 " model vdw 2.215 3.120 ... (remaining 38413 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=0.77 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.100 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5610 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 : 0.010 0.223 5136 Z= 0.650 Angle : 1.686 36.730 6974 Z= 0.897 Chirality : 0.111 2.008 790 Planarity : 0.012 0.190 881 Dihedral : 15.204 163.082 1859 Min Nonbonded Distance : 1.333 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 0.77 % Allowed : 1.35 % Favored : 97.88 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 3.03 % 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: -4.62 (0.27), residues: 621 helix: -3.24 (0.21), residues: 289 sheet: -3.17 (0.77), residues: 35 loop : -2.79 (0.31), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.105 0.006 TRP B 58 HIS 0.008 0.001 HIS A 121 PHE 0.028 0.003 PHE B 177 TYR 0.056 0.003 TYR A 57 ARG 0.013 0.001 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 181 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7274 (m-80) cc_final: 0.6975 (m-80) REVERT: A 47 LEU cc_start: 0.7122 (mp) cc_final: 0.6829 (mp) REVERT: A 56 LYS cc_start: 0.7179 (ptmt) cc_final: 0.6933 (pttt) REVERT: A 266 PHE cc_start: 0.7276 (p90) cc_final: 0.6101 (p90) REVERT: B 122 LYS cc_start: 0.7715 (tptt) cc_final: 0.7086 (tptp) REVERT: B 145 PHE cc_start: 0.6492 (t80) cc_final: 0.5935 (t80) REVERT: B 173 SER cc_start: 0.8682 (t) cc_final: 0.8273 (t) REVERT: B 221 PHE cc_start: 0.6836 (m-10) cc_final: 0.6629 (m-80) REVERT: B 261 TYR cc_start: 0.5351 (m-80) cc_final: 0.5020 (m-80) REVERT: B 280 THR cc_start: 0.7529 (m) cc_final: 0.6935 (m) outliers start: 4 outliers final: 0 residues processed: 185 average time/residue: 0.2034 time to fit residues: 45.9276 Evaluate side-chains 168 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 GLN B 212 HIS B 219 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.157437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.133925 restraints weight = 10083.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.137954 restraints weight = 6237.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.140759 restraints weight = 4332.886| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4134 r_free = 0.4134 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5136 Z= 0.216 Angle : 0.811 11.130 6974 Z= 0.405 Chirality : 0.050 0.264 790 Planarity : 0.008 0.069 881 Dihedral : 8.816 161.155 697 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.32 % Allowed : 13.13 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -3.20 (0.30), residues: 621 helix: -1.84 (0.27), residues: 281 sheet: -2.82 (0.84), residues: 33 loop : -2.27 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 58 HIS 0.003 0.001 HIS B 213 PHE 0.019 0.002 PHE A 266 TYR 0.018 0.002 TYR B 261 ARG 0.006 0.000 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 288 ARG cc_start: 0.6814 (mtm180) cc_final: 0.6600 (mtm110) REVERT: A 61 MET cc_start: 0.6956 (mmt) cc_final: 0.6683 (mmm) REVERT: A 65 ASN cc_start: 0.6827 (p0) cc_final: 0.6159 (p0) REVERT: A 144 LYS cc_start: 0.7351 (mmtt) cc_final: 0.6878 (mmtt) REVERT: A 266 PHE cc_start: 0.7942 (p90) cc_final: 0.7364 (p90) REVERT: B 66 GLN cc_start: 0.7593 (tp-100) cc_final: 0.7223 (tp-100) REVERT: B 122 LYS cc_start: 0.8217 (tptt) cc_final: 0.7924 (tptt) REVERT: B 125 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7630 (tm-30) REVERT: B 145 PHE cc_start: 0.7523 (t80) cc_final: 0.6967 (t80) REVERT: B 169 LEU cc_start: 0.7358 (tp) cc_final: 0.6875 (tp) REVERT: B 173 SER cc_start: 0.8262 (t) cc_final: 0.8029 (t) REVERT: B 219 HIS cc_start: 0.7042 (m90) cc_final: 0.6158 (t70) outliers start: 12 outliers final: 8 residues processed: 179 average time/residue: 0.2160 time to fit residues: 47.1135 Evaluate side-chains 175 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 281 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 0.0970 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.157426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.134125 restraints weight = 10120.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.138087 restraints weight = 6255.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.140792 restraints weight = 4348.184| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4142 r_free = 0.4142 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4142 r_free = 0.4142 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5136 Z= 0.207 Angle : 0.746 8.554 6974 Z= 0.378 Chirality : 0.048 0.213 790 Planarity : 0.007 0.073 881 Dihedral : 8.080 148.504 697 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.09 % Allowed : 18.73 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.68 (0.31), residues: 621 helix: -1.20 (0.29), residues: 281 sheet: -2.49 (0.90), residues: 28 loop : -2.27 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 58 HIS 0.004 0.001 HIS A 121 PHE 0.026 0.002 PHE B 148 TYR 0.017 0.002 TYR B 49 ARG 0.005 0.001 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7468 (m-80) cc_final: 0.6731 (m-80) REVERT: C 288 ARG cc_start: 0.6781 (mtm180) cc_final: 0.6547 (mtm110) REVERT: A 22 TYR cc_start: 0.7113 (m-80) cc_final: 0.6892 (t80) REVERT: A 56 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7249 (pttt) REVERT: A 74 MET cc_start: 0.7761 (tpp) cc_final: 0.7448 (tpp) REVERT: A 110 MET cc_start: 0.7667 (mmm) cc_final: 0.6998 (mmm) REVERT: A 114 LEU cc_start: 0.8578 (mm) cc_final: 0.8199 (mm) REVERT: A 177 PHE cc_start: 0.6269 (m-80) cc_final: 0.5833 (t80) REVERT: A 237 THR cc_start: 0.6188 (m) cc_final: 0.5900 (p) REVERT: A 266 PHE cc_start: 0.7911 (p90) cc_final: 0.7550 (p90) REVERT: A 298 ASP cc_start: 0.7235 (p0) cc_final: 0.7011 (p0) REVERT: B 49 TYR cc_start: 0.5744 (t80) cc_final: 0.5376 (t80) REVERT: B 66 GLN cc_start: 0.7633 (tp-100) cc_final: 0.7232 (tp-100) REVERT: B 112 GLU cc_start: 0.7344 (tt0) cc_final: 0.6071 (tp30) REVERT: B 115 ASP cc_start: 0.7167 (p0) cc_final: 0.6800 (p0) REVERT: B 122 LYS cc_start: 0.8252 (tptt) cc_final: 0.7931 (tptt) REVERT: B 125 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7544 (tm-30) REVERT: B 145 PHE cc_start: 0.7612 (t80) cc_final: 0.7235 (t80) REVERT: B 149 PHE cc_start: 0.7442 (m-80) cc_final: 0.7185 (m-80) REVERT: B 169 LEU cc_start: 0.7354 (tp) cc_final: 0.7007 (tp) REVERT: B 173 SER cc_start: 0.8340 (t) cc_final: 0.8130 (t) REVERT: B 174 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7209 (pt0) REVERT: B 191 ARG cc_start: 0.7973 (ttt180) cc_final: 0.7171 (ttt180) REVERT: B 219 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.6210 (t70) REVERT: B 221 PHE cc_start: 0.7453 (m-10) cc_final: 0.7210 (m-80) REVERT: B 248 ARG cc_start: 0.7731 (mtp85) cc_final: 0.7399 (mtp85) REVERT: B 261 TYR cc_start: 0.5999 (m-80) cc_final: 0.5781 (m-80) REVERT: B 275 ASP cc_start: 0.5378 (t0) cc_final: 0.5016 (t0) outliers start: 16 outliers final: 6 residues processed: 180 average time/residue: 0.2059 time to fit residues: 45.5090 Evaluate side-chains 176 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 245 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 0.0060 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 276 GLN ** B 54 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 = 0.4327 r_free = 0.4327 target = 0.156045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.133125 restraints weight = 10124.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.137225 restraints weight = 6137.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.140046 restraints weight = 4190.044| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5136 Z= 0.208 Angle : 0.722 7.853 6974 Z= 0.366 Chirality : 0.048 0.184 790 Planarity : 0.006 0.061 881 Dihedral : 7.431 130.518 697 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.09 % Allowed : 23.36 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.55 (0.32), residues: 621 helix: -1.04 (0.29), residues: 293 sheet: -2.42 (0.89), residues: 28 loop : -2.29 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 58 HIS 0.004 0.001 HIS A 121 PHE 0.017 0.001 PHE A 266 TYR 0.016 0.002 TYR B 55 ARG 0.003 0.001 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7443 (m-80) cc_final: 0.6702 (m-80) REVERT: A 20 VAL cc_start: 0.7176 (OUTLIER) cc_final: 0.6807 (p) REVERT: A 110 MET cc_start: 0.7665 (mmm) cc_final: 0.6937 (mmm) REVERT: A 114 LEU cc_start: 0.8470 (mm) cc_final: 0.7934 (mm) REVERT: A 135 LEU cc_start: 0.7838 (mt) cc_final: 0.7613 (mt) REVERT: A 171 ARG cc_start: 0.7438 (ttm110) cc_final: 0.7073 (ttm110) REVERT: A 175 LEU cc_start: 0.8893 (mt) cc_final: 0.8659 (mp) REVERT: A 278 ARG cc_start: 0.7464 (ttm170) cc_final: 0.7224 (ttm170) REVERT: A 298 ASP cc_start: 0.7345 (p0) cc_final: 0.7137 (p0) REVERT: B 66 GLN cc_start: 0.7598 (tp-100) cc_final: 0.7164 (tp-100) REVERT: B 112 GLU cc_start: 0.7380 (tt0) cc_final: 0.6121 (tp30) REVERT: B 115 ASP cc_start: 0.7159 (p0) cc_final: 0.6748 (p0) REVERT: B 125 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7594 (tm-30) REVERT: B 145 PHE cc_start: 0.7657 (t80) cc_final: 0.7038 (t80) REVERT: B 149 PHE cc_start: 0.7522 (m-80) cc_final: 0.7159 (m-80) REVERT: B 169 LEU cc_start: 0.7444 (tp) cc_final: 0.7059 (mt) REVERT: B 174 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7280 (pt0) REVERT: B 191 ARG cc_start: 0.7907 (ttt180) cc_final: 0.7168 (ttt180) REVERT: B 219 HIS cc_start: 0.7029 (OUTLIER) cc_final: 0.6182 (t70) REVERT: B 221 PHE cc_start: 0.7462 (m-10) cc_final: 0.7249 (m-80) REVERT: B 244 ARG cc_start: 0.7190 (ttp-110) cc_final: 0.6971 (ttp-110) outliers start: 16 outliers final: 7 residues processed: 179 average time/residue: 0.2045 time to fit residues: 44.9521 Evaluate side-chains 178 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 245 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.0040 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 213 GLN ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 HIS ** 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 = 0.4298 r_free = 0.4298 target = 0.153504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.130609 restraints weight = 10084.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.134660 restraints weight = 6102.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.137433 restraints weight = 4148.477| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4099 r_free = 0.4099 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4099 r_free = 0.4099 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5136 Z= 0.215 Angle : 0.734 9.993 6974 Z= 0.366 Chirality : 0.049 0.193 790 Planarity : 0.006 0.067 881 Dihedral : 6.894 112.058 697 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.67 % Allowed : 24.90 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.45 (0.31), residues: 621 helix: -0.92 (0.29), residues: 296 sheet: -2.97 (0.82), residues: 30 loop : -2.20 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 58 HIS 0.005 0.001 HIS A 121 PHE 0.017 0.001 PHE A 266 TYR 0.034 0.002 TYR A 204 ARG 0.006 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7493 (m-80) cc_final: 0.6833 (m-80) REVERT: A 20 VAL cc_start: 0.7279 (OUTLIER) cc_final: 0.6781 (p) REVERT: A 33 ILE cc_start: 0.8151 (pt) cc_final: 0.7638 (mm) REVERT: A 114 LEU cc_start: 0.8439 (mm) cc_final: 0.8110 (mm) REVERT: A 121 HIS cc_start: 0.7810 (m90) cc_final: 0.7261 (m90) REVERT: A 135 LEU cc_start: 0.8042 (mt) cc_final: 0.7820 (mt) REVERT: A 278 ARG cc_start: 0.7536 (ttm170) cc_final: 0.7311 (ttm170) REVERT: B 66 GLN cc_start: 0.7660 (tp-100) cc_final: 0.7279 (tp-100) REVERT: B 122 LYS cc_start: 0.8310 (tptt) cc_final: 0.7929 (tptt) REVERT: B 125 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7581 (tm-30) REVERT: B 145 PHE cc_start: 0.7726 (t80) cc_final: 0.7088 (t80) REVERT: B 149 PHE cc_start: 0.7650 (m-80) cc_final: 0.7337 (m-80) REVERT: B 156 GLN cc_start: 0.7043 (OUTLIER) cc_final: 0.6441 (pm20) REVERT: B 169 LEU cc_start: 0.7437 (tp) cc_final: 0.7196 (mt) REVERT: B 174 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7238 (pt0) REVERT: B 191 ARG cc_start: 0.7901 (ttt180) cc_final: 0.7163 (ttt180) REVERT: B 219 HIS cc_start: 0.7099 (OUTLIER) cc_final: 0.6262 (t70) REVERT: B 244 ARG cc_start: 0.7335 (ttp-110) cc_final: 0.6968 (ttp-110) REVERT: B 334 THR cc_start: 0.8358 (t) cc_final: 0.7994 (p) REVERT: B 338 GLU cc_start: 0.7102 (pp20) cc_final: 0.6880 (pp20) outliers start: 19 outliers final: 11 residues processed: 179 average time/residue: 0.2016 time to fit residues: 44.6100 Evaluate side-chains 185 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 245 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 28 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.154001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.130469 restraints weight = 10143.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.134637 restraints weight = 6131.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.137493 restraints weight = 4178.129| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4104 r_free = 0.4104 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4104 r_free = 0.4104 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5136 Z= 0.207 Angle : 0.731 12.137 6974 Z= 0.361 Chirality : 0.048 0.221 790 Planarity : 0.006 0.064 881 Dihedral : 6.676 102.509 697 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.86 % Allowed : 25.68 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.31 (0.32), residues: 621 helix: -0.73 (0.30), residues: 294 sheet: -3.00 (0.83), residues: 30 loop : -2.19 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 58 HIS 0.004 0.001 HIS A 121 PHE 0.018 0.002 PHE A 266 TYR 0.051 0.002 TYR A 204 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7428 (m-80) cc_final: 0.6893 (m-80) REVERT: A 20 VAL cc_start: 0.7416 (t) cc_final: 0.7100 (p) REVERT: A 56 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7146 (pttt) REVERT: A 89 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7177 (t0) REVERT: A 114 LEU cc_start: 0.8415 (mm) cc_final: 0.8042 (mm) REVERT: A 115 ARG cc_start: 0.7254 (mtt180) cc_final: 0.6870 (mtp180) REVERT: A 121 HIS cc_start: 0.7822 (m90) cc_final: 0.7282 (m90) REVERT: A 171 ARG cc_start: 0.7398 (ttm110) cc_final: 0.6837 (ttm110) REVERT: A 175 LEU cc_start: 0.8885 (mt) cc_final: 0.8635 (mt) REVERT: A 214 MET cc_start: 0.7900 (ttm) cc_final: 0.7601 (ttm) REVERT: A 250 ASP cc_start: 0.7587 (t0) cc_final: 0.7310 (t0) REVERT: A 278 ARG cc_start: 0.7560 (ttm170) cc_final: 0.7359 (ttm170) REVERT: B 66 GLN cc_start: 0.7681 (tp-100) cc_final: 0.7291 (tp-100) REVERT: B 112 GLU cc_start: 0.7200 (tt0) cc_final: 0.5688 (tp30) REVERT: B 122 LYS cc_start: 0.8335 (tptt) cc_final: 0.7948 (tptt) REVERT: B 125 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7590 (tm-30) REVERT: B 145 PHE cc_start: 0.7722 (t80) cc_final: 0.7034 (t80) REVERT: B 149 PHE cc_start: 0.7663 (m-80) cc_final: 0.7300 (m-80) REVERT: B 156 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6323 (pm20) REVERT: B 219 HIS cc_start: 0.7072 (OUTLIER) cc_final: 0.6235 (t70) REVERT: B 244 ARG cc_start: 0.7363 (ttp-110) cc_final: 0.6970 (ttp-110) REVERT: B 334 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.7999 (p) outliers start: 20 outliers final: 9 residues processed: 187 average time/residue: 0.1943 time to fit residues: 45.1954 Evaluate side-chains 192 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 334 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 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 = 0.4278 r_free = 0.4278 target = 0.151724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.128353 restraints weight = 10057.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.132386 restraints weight = 6078.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.135234 restraints weight = 4164.323| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4071 r_free = 0.4071 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4071 r_free = 0.4071 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5136 Z= 0.239 Angle : 0.782 14.026 6974 Z= 0.385 Chirality : 0.051 0.273 790 Planarity : 0.006 0.063 881 Dihedral : 6.624 93.939 697 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.21 % Allowed : 25.68 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.35 (0.32), residues: 621 helix: -0.74 (0.30), residues: 300 sheet: -3.22 (0.81), residues: 30 loop : -2.25 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 58 HIS 0.006 0.001 HIS A 121 PHE 0.023 0.002 PHE A 266 TYR 0.044 0.002 TYR A 204 ARG 0.004 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7470 (m-80) cc_final: 0.7194 (m-80) REVERT: A 20 VAL cc_start: 0.7512 (t) cc_final: 0.7292 (p) REVERT: A 33 ILE cc_start: 0.8187 (pt) cc_final: 0.7690 (mm) REVERT: A 65 ASN cc_start: 0.6663 (p0) cc_final: 0.5984 (p0) REVERT: A 89 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7204 (t0) REVERT: A 106 ILE cc_start: 0.8057 (tp) cc_final: 0.7789 (pt) REVERT: A 114 LEU cc_start: 0.8425 (mm) cc_final: 0.8066 (mm) REVERT: A 121 HIS cc_start: 0.7865 (m90) cc_final: 0.7408 (m90) REVERT: A 144 LYS cc_start: 0.7503 (mmtt) cc_final: 0.7042 (mmtt) REVERT: A 171 ARG cc_start: 0.7539 (ttm110) cc_final: 0.7022 (ttm110) REVERT: A 214 MET cc_start: 0.7721 (ttm) cc_final: 0.7472 (ttm) REVERT: A 268 CYS cc_start: 0.7474 (t) cc_final: 0.6750 (m) REVERT: B 66 GLN cc_start: 0.7655 (tp-100) cc_final: 0.7277 (tp-100) REVERT: B 112 GLU cc_start: 0.7139 (tt0) cc_final: 0.5586 (tp30) REVERT: B 122 LYS cc_start: 0.8382 (tptt) cc_final: 0.7995 (tptt) REVERT: B 125 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7596 (tm-30) REVERT: B 145 PHE cc_start: 0.7705 (t80) cc_final: 0.7019 (t80) REVERT: B 149 PHE cc_start: 0.7646 (m-80) cc_final: 0.7297 (m-80) REVERT: B 156 GLN cc_start: 0.6963 (OUTLIER) cc_final: 0.6342 (pm20) REVERT: B 219 HIS cc_start: 0.7110 (OUTLIER) cc_final: 0.6251 (t70) REVERT: B 334 THR cc_start: 0.8302 (t) cc_final: 0.7973 (p) REVERT: B 336 ILE cc_start: 0.6871 (mm) cc_final: 0.6636 (tt) REVERT: B 338 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6798 (pp20) outliers start: 27 outliers final: 14 residues processed: 191 average time/residue: 0.1947 time to fit residues: 46.2270 Evaluate side-chains 197 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 338 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 34 optimal weight: 0.0370 chunk 45 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.0570 chunk 32 optimal weight: 0.4980 chunk 46 optimal weight: 0.0970 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 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 = 0.4317 r_free = 0.4317 target = 0.155261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.132338 restraints weight = 10109.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.136458 restraints weight = 6121.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.139311 restraints weight = 4158.737| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5136 Z= 0.184 Angle : 0.769 13.151 6974 Z= 0.372 Chirality : 0.048 0.229 790 Planarity : 0.006 0.061 881 Dihedral : 6.471 91.304 697 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.47 % Allowed : 28.76 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.24 (0.32), residues: 621 helix: -0.70 (0.30), residues: 301 sheet: -3.18 (0.82), residues: 30 loop : -2.13 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 229 HIS 0.004 0.001 HIS A 121 PHE 0.017 0.002 PHE B 222 TYR 0.044 0.002 TYR A 204 ARG 0.008 0.001 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7323 (m-80) cc_final: 0.7046 (m-80) REVERT: A 20 VAL cc_start: 0.7524 (t) cc_final: 0.7264 (p) REVERT: A 114 LEU cc_start: 0.8403 (mm) cc_final: 0.8111 (mm) REVERT: A 158 HIS cc_start: 0.7721 (p-80) cc_final: 0.7455 (p-80) REVERT: A 171 ARG cc_start: 0.7554 (ttm110) cc_final: 0.6967 (ttm110) REVERT: A 268 CYS cc_start: 0.7402 (t) cc_final: 0.6712 (m) REVERT: B 66 GLN cc_start: 0.7605 (tp-100) cc_final: 0.7190 (tp-100) REVERT: B 112 GLU cc_start: 0.7108 (tt0) cc_final: 0.5594 (tp30) REVERT: B 122 LYS cc_start: 0.8360 (tptt) cc_final: 0.7973 (tptt) REVERT: B 125 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7568 (tm-30) REVERT: B 145 PHE cc_start: 0.7610 (t80) cc_final: 0.6843 (t80) REVERT: B 149 PHE cc_start: 0.7594 (m-80) cc_final: 0.7183 (m-80) REVERT: B 156 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6294 (pm20) REVERT: B 219 HIS cc_start: 0.7027 (OUTLIER) cc_final: 0.6226 (t70) REVERT: B 244 ARG cc_start: 0.7035 (ttp-110) cc_final: 0.6689 (ttp-110) REVERT: B 331 LYS cc_start: 0.8152 (mtmm) cc_final: 0.7882 (mtmm) REVERT: B 334 THR cc_start: 0.8267 (t) cc_final: 0.7945 (p) REVERT: B 336 ILE cc_start: 0.6853 (mm) cc_final: 0.6605 (tt) REVERT: B 338 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6658 (pp20) outliers start: 18 outliers final: 13 residues processed: 188 average time/residue: 0.2257 time to fit residues: 53.3685 Evaluate side-chains 195 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 338 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 60 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.152843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.129392 restraints weight = 9979.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.133527 restraints weight = 6047.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.136360 restraints weight = 4134.853| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5136 Z= 0.223 Angle : 0.801 16.073 6974 Z= 0.391 Chirality : 0.050 0.235 790 Planarity : 0.006 0.058 881 Dihedral : 6.490 88.418 697 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 4.25 % Allowed : 27.99 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.26 (0.32), residues: 621 helix: -0.72 (0.30), residues: 301 sheet: -3.09 (0.81), residues: 30 loop : -2.15 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP B 58 HIS 0.005 0.001 HIS A 121 PHE 0.020 0.001 PHE A 177 TYR 0.038 0.002 TYR A 204 ARG 0.007 0.001 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 VAL cc_start: 0.7344 (t) cc_final: 0.7044 (p) REVERT: A 114 LEU cc_start: 0.8428 (mm) cc_final: 0.8056 (mm) REVERT: A 121 HIS cc_start: 0.7784 (m90) cc_final: 0.7305 (m90) REVERT: A 144 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.7043 (mmmt) REVERT: A 158 HIS cc_start: 0.7723 (p-80) cc_final: 0.7492 (p-80) REVERT: A 171 ARG cc_start: 0.7586 (ttm110) cc_final: 0.6981 (ttm110) REVERT: A 215 GLU cc_start: 0.7743 (mp0) cc_final: 0.7100 (mp0) REVERT: A 268 CYS cc_start: 0.7457 (t) cc_final: 0.6765 (m) REVERT: B 66 GLN cc_start: 0.7644 (tp-100) cc_final: 0.7226 (tp-100) REVERT: B 112 GLU cc_start: 0.7160 (tt0) cc_final: 0.5645 (tp30) REVERT: B 122 LYS cc_start: 0.8377 (tptt) cc_final: 0.7989 (tptt) REVERT: B 125 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7585 (tm-30) REVERT: B 145 PHE cc_start: 0.7640 (t80) cc_final: 0.6860 (t80) REVERT: B 149 PHE cc_start: 0.7690 (m-80) cc_final: 0.7279 (m-80) REVERT: B 156 GLN cc_start: 0.6963 (OUTLIER) cc_final: 0.6252 (pm20) REVERT: B 169 LEU cc_start: 0.7495 (tp) cc_final: 0.7093 (tp) REVERT: B 219 HIS cc_start: 0.6978 (OUTLIER) cc_final: 0.6133 (t70) REVERT: B 244 ARG cc_start: 0.7163 (ttp-110) cc_final: 0.6812 (ttp-110) REVERT: B 248 ARG cc_start: 0.7907 (mtp85) cc_final: 0.7598 (mmp80) REVERT: B 331 LYS cc_start: 0.8223 (mtmm) cc_final: 0.7917 (mtmm) REVERT: B 334 THR cc_start: 0.8290 (t) cc_final: 0.7963 (p) REVERT: B 336 ILE cc_start: 0.6852 (mm) cc_final: 0.6601 (tt) REVERT: B 338 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6643 (pp20) outliers start: 22 outliers final: 15 residues processed: 189 average time/residue: 0.1925 time to fit residues: 44.9847 Evaluate side-chains 198 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 338 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 37 optimal weight: 0.0570 chunk 19 optimal weight: 6.9990 chunk 61 optimal weight: 0.0770 chunk 31 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.153469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.130044 restraints weight = 10016.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.134099 restraints weight = 6097.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.136869 restraints weight = 4201.228| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.6009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5136 Z= 0.222 Angle : 0.813 15.809 6974 Z= 0.394 Chirality : 0.050 0.232 790 Planarity : 0.006 0.054 881 Dihedral : 6.477 87.607 697 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 4.25 % Allowed : 28.96 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.30 (0.32), residues: 621 helix: -0.80 (0.29), residues: 307 sheet: -3.18 (0.81), residues: 30 loop : -2.12 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP B 58 HIS 0.005 0.001 HIS A 121 PHE 0.021 0.002 PHE A 177 TYR 0.033 0.002 TYR A 204 ARG 0.006 0.001 ARG B 244 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 VAL cc_start: 0.7386 (t) cc_final: 0.7107 (p) REVERT: A 114 LEU cc_start: 0.8413 (mm) cc_final: 0.8128 (mm) REVERT: A 171 ARG cc_start: 0.7579 (ttm110) cc_final: 0.6987 (ttm110) REVERT: A 215 GLU cc_start: 0.7727 (mp0) cc_final: 0.7060 (mp0) REVERT: B 66 GLN cc_start: 0.7622 (tp-100) cc_final: 0.7206 (tp-100) REVERT: B 112 GLU cc_start: 0.7147 (tt0) cc_final: 0.5617 (tp30) REVERT: B 122 LYS cc_start: 0.8367 (tptt) cc_final: 0.7988 (tptt) REVERT: B 125 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7589 (tm-30) REVERT: B 145 PHE cc_start: 0.7627 (t80) cc_final: 0.6803 (t80) REVERT: B 149 PHE cc_start: 0.7652 (m-80) cc_final: 0.7270 (m-80) REVERT: B 156 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6198 (pm20) REVERT: B 191 ARG cc_start: 0.7748 (ttt180) cc_final: 0.7048 (ttt180) REVERT: B 219 HIS cc_start: 0.6929 (OUTLIER) cc_final: 0.6081 (t70) REVERT: B 244 ARG cc_start: 0.7152 (ttp-110) cc_final: 0.6809 (ttp-110) REVERT: B 248 ARG cc_start: 0.7843 (mtp85) cc_final: 0.7632 (mmp80) REVERT: B 331 LYS cc_start: 0.8195 (mtmm) cc_final: 0.7987 (mtmm) REVERT: B 334 THR cc_start: 0.8284 (t) cc_final: 0.7974 (p) REVERT: B 336 ILE cc_start: 0.6846 (mm) cc_final: 0.6614 (tt) outliers start: 22 outliers final: 18 residues processed: 186 average time/residue: 0.2141 time to fit residues: 48.6046 Evaluate side-chains 193 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 288 ARG Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 234 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 15 optimal weight: 3.9990 chunk 58 optimal weight: 0.0040 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 61 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.0670 chunk 31 optimal weight: 0.6980 overall best weight: 0.4330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.154795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.131399 restraints weight = 10146.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.135592 restraints weight = 6124.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.138455 restraints weight = 4169.656| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.6118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5136 Z= 0.196 Angle : 0.792 15.206 6974 Z= 0.382 Chirality : 0.049 0.233 790 Planarity : 0.006 0.052 881 Dihedral : 6.394 86.422 697 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.47 % Allowed : 30.50 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.18 (0.33), residues: 621 helix: -0.73 (0.30), residues: 308 sheet: -3.03 (0.83), residues: 30 loop : -2.04 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 229 HIS 0.004 0.001 HIS A 121 PHE 0.019 0.001 PHE A 177 TYR 0.032 0.002 TYR A 204 ARG 0.006 0.001 ARG B 244 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2255.42 seconds wall clock time: 40 minutes 56.85 seconds (2456.85 seconds total)