Starting phenix.real_space_refine on Wed Mar 12 09:29:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e7z_31005/03_2025/7e7z_31005.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e7z_31005/03_2025/7e7z_31005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e7z_31005/03_2025/7e7z_31005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e7z_31005/03_2025/7e7z_31005.map" model { file = "/net/cci-nas-00/data/ceres_data/7e7z_31005/03_2025/7e7z_31005.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e7z_31005/03_2025/7e7z_31005.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5152 2.51 5 N 1264 2.21 5 O 1336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7808 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1952 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 1 Chain: "B" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1952 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 1 Chain: "C" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1952 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 1 Chain: "D" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1952 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 1 Time building chain proxies: 5.99, per 1000 atoms: 0.77 Number of scatterers: 7808 At special positions: 0 Unit cell: (111.251, 111.251, 78.1763, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1336 8.00 N 1264 7.00 C 5152 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: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1880 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 82.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 166 through 177 removed outlier: 4.277A pdb=" N ARG A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 207 Processing helix chain 'A' and resid 227 through 249 Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 282 Proline residue: A 272 - end of helix removed outlier: 3.769A pdb=" N ASN A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 4.115A pdb=" N VAL A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 removed outlier: 3.735A pdb=" N ARG A 305 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 320 removed outlier: 3.850A pdb=" N ARG A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 346 Processing helix chain 'A' and resid 356 through 369 removed outlier: 4.249A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 399 removed outlier: 4.040A pdb=" N SER A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 417 removed outlier: 4.610A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 417 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 177 removed outlier: 4.266A pdb=" N ARG B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 207 Processing helix chain 'B' and resid 227 through 249 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 260 through 282 Proline residue: B 272 - end of helix removed outlier: 3.759A pdb=" N ASN B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 296 removed outlier: 4.138A pdb=" N VAL B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 removed outlier: 3.739A pdb=" N ARG B 305 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.830A pdb=" N ARG B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 346 Processing helix chain 'B' and resid 356 through 369 removed outlier: 4.230A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 399 removed outlier: 4.020A pdb=" N SER B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 417 removed outlier: 4.666A pdb=" N VAL B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN B 417 " --> pdb=" O TYR B 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 177 removed outlier: 4.315A pdb=" N ARG C 170 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA C 174 " --> pdb=" O ARG C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 205 Processing helix chain 'C' and resid 227 through 249 removed outlier: 3.784A pdb=" N CYS C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 260 removed outlier: 3.619A pdb=" N ARG C 259 " --> pdb=" O TYR C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 282 Proline residue: C 272 - end of helix removed outlier: 3.816A pdb=" N ASN C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 297 through 305 removed outlier: 3.743A pdb=" N ARG C 305 " --> pdb=" O LYS C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 320 removed outlier: 3.799A pdb=" N ARG C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 346 Processing helix chain 'C' and resid 356 through 369 removed outlier: 4.158A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 399 removed outlier: 4.024A pdb=" N SER C 391 " --> pdb=" O GLY C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 417 removed outlier: 4.594A pdb=" N VAL C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN C 417 " --> pdb=" O TYR C 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 177 removed outlier: 4.275A pdb=" N ARG D 170 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 207 Processing helix chain 'D' and resid 227 through 249 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 282 Proline residue: D 272 - end of helix removed outlier: 3.768A pdb=" N ASN D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 removed outlier: 4.129A pdb=" N VAL D 290 " --> pdb=" O SER D 286 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR D 291 " --> pdb=" O GLY D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 removed outlier: 3.565A pdb=" N PHE D 301 " --> pdb=" O PHE D 298 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG D 305 " --> pdb=" O LYS D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 320 removed outlier: 3.840A pdb=" N ARG D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 346 Processing helix chain 'D' and resid 356 through 369 removed outlier: 4.260A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 399 removed outlier: 4.016A pdb=" N SER D 391 " --> pdb=" O GLY D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 417 removed outlier: 4.618A pdb=" N VAL D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN D 417 " --> pdb=" O TYR D 413 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2351 1.35 - 1.46: 2134 1.46 - 1.58: 3423 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 8000 Sorted by residual: bond pdb=" C LEU A 271 " pdb=" N PRO A 272 " ideal model delta sigma weight residual 1.334 1.364 -0.030 1.51e-02 4.39e+03 3.82e+00 bond pdb=" C LEU C 400 " pdb=" N PRO C 401 " ideal model delta sigma weight residual 1.332 1.340 -0.008 8.90e-03 1.26e+04 7.70e-01 bond pdb=" C LEU D 400 " pdb=" N PRO D 401 " ideal model delta sigma weight residual 1.332 1.340 -0.008 8.90e-03 1.26e+04 7.45e-01 bond pdb=" C LEU B 400 " pdb=" N PRO B 401 " ideal model delta sigma weight residual 1.332 1.340 -0.008 8.90e-03 1.26e+04 7.33e-01 bond pdb=" C LEU A 400 " pdb=" N PRO A 401 " ideal model delta sigma weight residual 1.332 1.340 -0.007 8.90e-03 1.26e+04 6.56e-01 ... (remaining 7995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 10690 1.73 - 3.45: 141 3.45 - 5.18: 29 5.18 - 6.90: 0 6.90 - 8.63: 4 Bond angle restraints: 10864 Sorted by residual: angle pdb=" N VAL C 171 " pdb=" CA VAL C 171 " pdb=" C VAL C 171 " ideal model delta sigma weight residual 113.39 108.45 4.94 1.47e+00 4.63e-01 1.13e+01 angle pdb=" CB MET D 262 " pdb=" CG MET D 262 " pdb=" SD MET D 262 " ideal model delta sigma weight residual 112.70 121.33 -8.63 3.00e+00 1.11e-01 8.27e+00 angle pdb=" CB MET C 262 " pdb=" CG MET C 262 " pdb=" SD MET C 262 " ideal model delta sigma weight residual 112.70 121.11 -8.41 3.00e+00 1.11e-01 7.86e+00 angle pdb=" CB MET B 262 " pdb=" CG MET B 262 " pdb=" SD MET B 262 " ideal model delta sigma weight residual 112.70 121.02 -8.32 3.00e+00 1.11e-01 7.69e+00 angle pdb=" CB MET A 262 " pdb=" CG MET A 262 " pdb=" SD MET A 262 " ideal model delta sigma weight residual 112.70 121.02 -8.32 3.00e+00 1.11e-01 7.69e+00 ... (remaining 10859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 4150 16.05 - 32.10: 412 32.10 - 48.15: 94 48.15 - 64.20: 9 64.20 - 80.25: 7 Dihedral angle restraints: 4672 sinusoidal: 1760 harmonic: 2912 Sorted by residual: dihedral pdb=" CA ALA B 226 " pdb=" C ALA B 226 " pdb=" N VAL B 227 " pdb=" CA VAL B 227 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ALA A 226 " pdb=" C ALA A 226 " pdb=" N VAL A 227 " pdb=" CA VAL A 227 " ideal model delta harmonic sigma weight residual 180.00 155.93 24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ALA D 226 " pdb=" C ALA D 226 " pdb=" N VAL D 227 " pdb=" CA VAL D 227 " ideal model delta harmonic sigma weight residual 180.00 156.75 23.25 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 4669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 749 0.026 - 0.052: 321 0.052 - 0.078: 167 0.078 - 0.104: 43 0.104 - 0.130: 12 Chirality restraints: 1292 Sorted by residual: chirality pdb=" CA VAL D 227 " pdb=" N VAL D 227 " pdb=" C VAL D 227 " pdb=" CB VAL D 227 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL A 227 " pdb=" N VAL A 227 " pdb=" C VAL A 227 " pdb=" CB VAL A 227 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CB VAL A 297 " pdb=" CA VAL A 297 " pdb=" CG1 VAL A 297 " pdb=" CG2 VAL A 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.53e-01 ... (remaining 1289 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 271 " 0.043 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO B 272 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 271 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO D 272 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 272 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 272 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 240 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C PHE D 240 " 0.034 2.00e-02 2.50e+03 pdb=" O PHE D 240 " -0.013 2.00e-02 2.50e+03 pdb=" N THR D 241 " -0.011 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1619 2.77 - 3.30: 8082 3.30 - 3.84: 12863 3.84 - 4.37: 14658 4.37 - 4.90: 25308 Nonbonded interactions: 62530 Sorted by model distance: nonbonded pdb=" O MET D 238 " pdb=" OG1 THR D 241 " model vdw 2.240 3.040 nonbonded pdb=" O MET B 238 " pdb=" OG1 THR B 241 " model vdw 2.242 3.040 nonbonded pdb=" O MET A 238 " pdb=" OG1 THR A 241 " model vdw 2.242 3.040 nonbonded pdb=" OE2 GLU C 205 " pdb=" NH2 ARG C 296 " model vdw 2.254 3.120 nonbonded pdb=" OG SER C 181 " pdb=" N THR C 182 " model vdw 2.289 3.120 ... (remaining 62525 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.420 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 : 0.002 0.030 8000 Z= 0.131 Angle : 0.511 8.627 10864 Z= 0.274 Chirality : 0.037 0.130 1292 Planarity : 0.005 0.064 1316 Dihedral : 13.400 80.246 2792 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 976 helix: 0.79 (0.19), residues: 732 sheet: None (None), residues: 0 loop : -2.76 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 362 HIS 0.001 0.000 HIS C 414 PHE 0.006 0.001 PHE B 343 TYR 0.014 0.001 TYR D 188 ARG 0.002 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LYS cc_start: 0.8468 (mtmt) cc_final: 0.8113 (mttp) REVERT: B 379 LYS cc_start: 0.8460 (mtmt) cc_final: 0.7860 (mttm) REVERT: C 318 LYS cc_start: 0.8522 (ttpp) cc_final: 0.8229 (ttpp) REVERT: C 333 MET cc_start: 0.8069 (ttm) cc_final: 0.7660 (ttt) REVERT: C 379 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8077 (mttm) REVERT: D 318 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8297 (ttpp) REVERT: D 379 LYS cc_start: 0.8420 (mtmt) cc_final: 0.8057 (mttp) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2114 time to fit residues: 37.8143 Evaluate side-chains 103 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 20.0000 chunk 49 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.0020 chunk 45 optimal weight: 0.1980 chunk 56 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.198965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.159848 restraints weight = 7989.495| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.38 r_work: 0.3231 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8000 Z= 0.166 Angle : 0.526 4.863 10864 Z= 0.285 Chirality : 0.040 0.151 1292 Planarity : 0.005 0.054 1316 Dihedral : 3.988 24.907 1088 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.94 % Allowed : 9.86 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.27), residues: 976 helix: 1.39 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -2.66 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 362 HIS 0.001 0.001 HIS B 414 PHE 0.011 0.001 PHE B 289 TYR 0.014 0.001 TYR C 188 ARG 0.004 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.6229 (mmt) cc_final: 0.5590 (ptm) REVERT: B 379 LYS cc_start: 0.8859 (mtmt) cc_final: 0.8485 (mttm) REVERT: C 318 LYS cc_start: 0.8893 (ttpp) cc_final: 0.8495 (ttpp) REVERT: C 333 MET cc_start: 0.8747 (ttm) cc_final: 0.8506 (mtp) REVERT: C 379 LYS cc_start: 0.8851 (mtmt) cc_final: 0.8423 (mttm) REVERT: C 396 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7485 (tp) REVERT: D 238 MET cc_start: 0.6250 (mmt) cc_final: 0.5592 (ptm) REVERT: D 298 PHE cc_start: 0.7773 (m-10) cc_final: 0.7544 (m-10) REVERT: D 318 LYS cc_start: 0.8833 (ttpp) cc_final: 0.8446 (ttpp) REVERT: D 353 LYS cc_start: 0.8894 (mttt) cc_final: 0.8674 (mttt) outliers start: 8 outliers final: 3 residues processed: 115 average time/residue: 0.2213 time to fit residues: 33.6764 Evaluate side-chains 106 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 300 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 53 optimal weight: 0.0040 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 0.0570 chunk 60 optimal weight: 0.5980 chunk 42 optimal weight: 0.0970 chunk 55 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.2908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN B 416 ASN C 416 ASN D 416 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.201659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.176667 restraints weight = 8078.101| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.25 r_work: 0.3439 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8000 Z= 0.139 Angle : 0.483 5.247 10864 Z= 0.260 Chirality : 0.039 0.129 1292 Planarity : 0.005 0.053 1316 Dihedral : 3.809 23.089 1088 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.41 % Allowed : 12.21 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.27), residues: 976 helix: 1.74 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -2.69 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 362 HIS 0.001 0.000 HIS D 414 PHE 0.010 0.001 PHE D 289 TYR 0.012 0.001 TYR D 188 ARG 0.003 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.6533 (mmt) cc_final: 0.5903 (ptt) REVERT: A 289 PHE cc_start: 0.8015 (t80) cc_final: 0.7811 (t80) REVERT: A 295 PHE cc_start: 0.8499 (m-80) cc_final: 0.8296 (m-80) REVERT: A 300 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8384 (tt) REVERT: B 238 MET cc_start: 0.6633 (mmt) cc_final: 0.5915 (ptt) REVERT: C 300 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8443 (tt) REVERT: C 318 LYS cc_start: 0.8972 (ttpp) cc_final: 0.8586 (ttpp) REVERT: D 238 MET cc_start: 0.6578 (mmt) cc_final: 0.5920 (ptt) REVERT: D 318 LYS cc_start: 0.8941 (ttpp) cc_final: 0.8572 (ttpp) outliers start: 12 outliers final: 5 residues processed: 112 average time/residue: 0.2087 time to fit residues: 31.6205 Evaluate side-chains 106 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 300 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 76 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 1 optimal weight: 0.0270 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 92 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 0.0020 overall best weight: 0.1846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.206163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.185935 restraints weight = 8040.624| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 1.09 r_work: 0.3720 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8000 Z= 0.128 Angle : 0.462 4.703 10864 Z= 0.250 Chirality : 0.038 0.128 1292 Planarity : 0.004 0.052 1316 Dihedral : 3.710 21.492 1088 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.76 % Allowed : 11.62 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.27), residues: 976 helix: 1.93 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -2.63 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 362 HIS 0.001 0.000 HIS C 414 PHE 0.007 0.001 PHE B 289 TYR 0.011 0.001 TYR D 188 ARG 0.002 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 LYS cc_start: 0.8822 (tttp) cc_final: 0.8556 (ttpp) REVERT: B 300 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8354 (tt) REVERT: C 300 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8540 (tt) REVERT: C 318 LYS cc_start: 0.8846 (ttpp) cc_final: 0.8605 (ttpp) REVERT: D 298 PHE cc_start: 0.7828 (m-10) cc_final: 0.7469 (m-10) REVERT: D 318 LYS cc_start: 0.8860 (ttpp) cc_final: 0.8608 (ttpp) outliers start: 15 outliers final: 7 residues processed: 106 average time/residue: 0.1943 time to fit residues: 28.6949 Evaluate side-chains 101 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 44 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 12 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.197595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.158079 restraints weight = 7862.858| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.99 r_work: 0.3130 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8000 Z= 0.190 Angle : 0.504 4.648 10864 Z= 0.271 Chirality : 0.040 0.133 1292 Planarity : 0.004 0.052 1316 Dihedral : 3.763 24.207 1088 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.53 % Allowed : 13.03 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.27), residues: 976 helix: 1.94 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -2.61 (0.36), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 362 HIS 0.001 0.000 HIS C 414 PHE 0.014 0.001 PHE C 289 TYR 0.015 0.001 TYR A 188 ARG 0.004 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LYS cc_start: 0.8959 (mtmt) cc_final: 0.8611 (mttp) REVERT: C 318 LYS cc_start: 0.8835 (ttpp) cc_final: 0.8451 (ttpp) REVERT: D 318 LYS cc_start: 0.8773 (ttpp) cc_final: 0.8421 (ttpp) REVERT: D 379 LYS cc_start: 0.8945 (mtmt) cc_final: 0.8590 (mttp) outliers start: 13 outliers final: 9 residues processed: 119 average time/residue: 0.1895 time to fit residues: 31.2310 Evaluate side-chains 122 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 300 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 40 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.198380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.176462 restraints weight = 7911.241| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.10 r_work: 0.3484 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8000 Z= 0.183 Angle : 0.503 6.465 10864 Z= 0.267 Chirality : 0.039 0.136 1292 Planarity : 0.004 0.051 1316 Dihedral : 3.796 25.072 1088 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.64 % Allowed : 14.20 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.27), residues: 976 helix: 1.98 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -2.58 (0.35), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 362 HIS 0.001 0.000 HIS C 414 PHE 0.009 0.001 PHE B 289 TYR 0.015 0.001 TYR D 188 ARG 0.003 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LYS cc_start: 0.8614 (mtmt) cc_final: 0.8332 (mttp) REVERT: C 318 LYS cc_start: 0.8867 (ttpp) cc_final: 0.8551 (ttpp) REVERT: D 318 LYS cc_start: 0.8888 (ttpp) cc_final: 0.8557 (ttpp) REVERT: D 379 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8371 (mttp) outliers start: 14 outliers final: 12 residues processed: 101 average time/residue: 0.3567 time to fit residues: 52.6672 Evaluate side-chains 106 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 300 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 60 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 17 optimal weight: 0.0970 chunk 13 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.198329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.133253 restraints weight = 7785.474| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.90 r_work: 0.3139 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8000 Z= 0.175 Angle : 0.499 5.610 10864 Z= 0.265 Chirality : 0.039 0.135 1292 Planarity : 0.004 0.050 1316 Dihedral : 3.790 25.229 1088 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.76 % Allowed : 14.55 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.27), residues: 976 helix: 2.03 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -2.54 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 362 HIS 0.001 0.000 HIS C 414 PHE 0.008 0.001 PHE B 343 TYR 0.015 0.001 TYR D 188 ARG 0.003 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LYS cc_start: 0.9011 (mtmt) cc_final: 0.8587 (mttp) REVERT: C 318 LYS cc_start: 0.8290 (ttpp) cc_final: 0.7905 (ttpp) REVERT: D 318 LYS cc_start: 0.8217 (ttpp) cc_final: 0.7836 (ttpp) REVERT: D 379 LYS cc_start: 0.8987 (mtmt) cc_final: 0.8559 (mttp) outliers start: 15 outliers final: 14 residues processed: 102 average time/residue: 0.2086 time to fit residues: 29.1017 Evaluate side-chains 110 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 300 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 0.0070 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.192577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.149835 restraints weight = 7850.300| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.66 r_work: 0.3229 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8000 Z= 0.214 Angle : 0.524 5.354 10864 Z= 0.279 Chirality : 0.040 0.137 1292 Planarity : 0.004 0.050 1316 Dihedral : 3.899 27.122 1088 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.88 % Allowed : 14.44 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.27), residues: 976 helix: 2.04 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -2.53 (0.35), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 362 HIS 0.001 0.000 HIS C 414 PHE 0.009 0.001 PHE A 343 TYR 0.017 0.001 TYR D 188 ARG 0.003 0.000 ARG D 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 CYS cc_start: 0.8445 (m) cc_final: 0.8117 (m) REVERT: A 289 PHE cc_start: 0.7807 (t80) cc_final: 0.7583 (t80) REVERT: A 379 LYS cc_start: 0.9163 (mtmt) cc_final: 0.8677 (mttm) REVERT: B 379 LYS cc_start: 0.9057 (mtmt) cc_final: 0.8655 (mttp) REVERT: C 318 LYS cc_start: 0.8514 (ttpp) cc_final: 0.8134 (ttpp) REVERT: C 379 LYS cc_start: 0.9044 (mtmt) cc_final: 0.8609 (mttp) REVERT: D 231 CYS cc_start: 0.8434 (m) cc_final: 0.8130 (m) REVERT: D 318 LYS cc_start: 0.8495 (ttpp) cc_final: 0.8087 (ttpp) REVERT: D 342 MET cc_start: 0.8782 (mmm) cc_final: 0.8498 (mmm) REVERT: D 379 LYS cc_start: 0.9116 (mtmt) cc_final: 0.8719 (mttm) outliers start: 16 outliers final: 15 residues processed: 120 average time/residue: 0.2285 time to fit residues: 37.4308 Evaluate side-chains 125 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 93 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 20.0000 chunk 71 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.196322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 146)---------------| | r_work = 0.3449 r_free = 0.3449 target = 0.135791 restraints weight = 7913.523| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.22 r_work: 0.3078 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8000 Z= 0.163 Angle : 0.492 6.008 10864 Z= 0.262 Chirality : 0.039 0.137 1292 Planarity : 0.004 0.050 1316 Dihedral : 3.832 26.030 1088 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.53 % Allowed : 15.02 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.27), residues: 976 helix: 2.14 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -2.54 (0.35), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 362 HIS 0.001 0.000 HIS D 414 PHE 0.010 0.001 PHE A 329 TYR 0.015 0.001 TYR A 188 ARG 0.007 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 PHE cc_start: 0.7662 (t80) cc_final: 0.7414 (t80) REVERT: A 379 LYS cc_start: 0.9100 (mtmt) cc_final: 0.8682 (mttm) REVERT: B 231 CYS cc_start: 0.8367 (m) cc_final: 0.7936 (m) REVERT: B 379 LYS cc_start: 0.8935 (mtmt) cc_final: 0.8532 (mttp) REVERT: C 231 CYS cc_start: 0.8460 (m) cc_final: 0.8143 (m) REVERT: C 318 LYS cc_start: 0.8385 (ttpp) cc_final: 0.8020 (ttpp) REVERT: C 379 LYS cc_start: 0.8940 (mtmt) cc_final: 0.8530 (mttp) REVERT: D 318 LYS cc_start: 0.8340 (ttpp) cc_final: 0.7953 (ttpp) REVERT: D 379 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8596 (mttm) outliers start: 13 outliers final: 13 residues processed: 103 average time/residue: 0.3067 time to fit residues: 45.0860 Evaluate side-chains 109 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.0770 chunk 53 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.196592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.149116 restraints weight = 7793.545| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.59 r_work: 0.3268 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8000 Z= 0.192 Angle : 0.508 5.805 10864 Z= 0.270 Chirality : 0.040 0.142 1292 Planarity : 0.004 0.049 1316 Dihedral : 3.838 26.302 1088 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.64 % Allowed : 15.14 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.27), residues: 976 helix: 2.11 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -2.53 (0.35), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 362 HIS 0.001 0.000 HIS C 414 PHE 0.009 0.001 PHE B 343 TYR 0.016 0.001 TYR D 188 ARG 0.006 0.000 ARG B 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 PHE cc_start: 0.7715 (t80) cc_final: 0.7418 (t80) REVERT: A 379 LYS cc_start: 0.9070 (mtmt) cc_final: 0.8632 (mttp) REVERT: B 379 LYS cc_start: 0.8990 (mtmt) cc_final: 0.8583 (mttp) REVERT: C 318 LYS cc_start: 0.8425 (ttpp) cc_final: 0.8053 (ttpp) REVERT: C 379 LYS cc_start: 0.8952 (mtmt) cc_final: 0.8536 (mttp) REVERT: D 318 LYS cc_start: 0.8391 (ttpp) cc_final: 0.7976 (ttpp) REVERT: D 379 LYS cc_start: 0.9040 (mtmt) cc_final: 0.8616 (mttm) outliers start: 14 outliers final: 14 residues processed: 107 average time/residue: 0.1849 time to fit residues: 27.4088 Evaluate side-chains 116 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 2.9990 chunk 61 optimal weight: 0.0470 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.0170 chunk 55 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.198497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.151436 restraints weight = 7794.811| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.59 r_work: 0.3214 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8000 Z= 0.164 Angle : 0.500 5.909 10864 Z= 0.265 Chirality : 0.039 0.147 1292 Planarity : 0.004 0.049 1316 Dihedral : 3.812 25.779 1088 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.64 % Allowed : 15.02 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.27), residues: 976 helix: 2.15 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -2.54 (0.35), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 362 HIS 0.001 0.000 HIS C 414 PHE 0.009 0.001 PHE C 289 TYR 0.014 0.001 TYR D 188 ARG 0.005 0.000 ARG B 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4760.77 seconds wall clock time: 85 minutes 6.62 seconds (5106.62 seconds total)