Starting phenix.real_space_refine on Tue Feb 11 15:19:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vq3_32084/02_2025/7vq3_32084.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vq3_32084/02_2025/7vq3_32084.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/7vq3_32084/02_2025/7vq3_32084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vq3_32084/02_2025/7vq3_32084.map" model { file = "/net/cci-nas-00/data/ceres_data/7vq3_32084/02_2025/7vq3_32084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vq3_32084/02_2025/7vq3_32084.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= -0.000 sd= 0.005 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 34 5.16 5 C 4070 2.51 5 N 1052 2.21 5 O 1150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 6306 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3153 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Restraints were copied for chains: B Time building chain proxies: 4.74, per 1000 atoms: 0.75 Number of scatterers: 6306 At special positions: 0 Unit cell: (84.162, 84.162, 109.512, 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 34 16.00 O 1150 8.00 N 1052 7.00 C 4070 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: 1.50 Conformation dependent library (CDL) restraints added in 945.3 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 84.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 1 through 18 removed outlier: 3.531A pdb=" N ASP A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.709A pdb=" N GLY A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 Processing helix chain 'A' and resid 69 through 102 removed outlier: 3.854A pdb=" N THR A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 125 Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 134 through 151 Processing helix chain 'A' and resid 158 through 183 removed outlier: 3.673A pdb=" N GLU A 163 " --> pdb=" O MET A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 214 Processing helix chain 'A' and resid 223 through 241 removed outlier: 4.395A pdb=" N ARG A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 241 " --> pdb=" O LYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 removed outlier: 3.543A pdb=" N ASN A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 294 removed outlier: 3.640A pdb=" N TYR A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 removed outlier: 4.030A pdb=" N LYS A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 330 removed outlier: 3.658A pdb=" N LEU A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 removed outlier: 4.206A pdb=" N ILE A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 344 " --> pdb=" O HIS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 398 Processing helix chain 'B' and resid 2 through 18 removed outlier: 3.531A pdb=" N ASP B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 41 removed outlier: 3.709A pdb=" N GLY B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 66 Processing helix chain 'B' and resid 69 through 102 removed outlier: 3.854A pdb=" N THR B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 125 Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 158 through 183 removed outlier: 3.673A pdb=" N GLU B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 214 Processing helix chain 'B' and resid 223 through 241 removed outlier: 4.395A pdb=" N ARG B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 254 removed outlier: 3.543A pdb=" N ASN B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 294 removed outlier: 3.640A pdb=" N TYR B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 305 removed outlier: 4.030A pdb=" N LYS B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 330 removed outlier: 3.658A pdb=" N LEU B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 356 removed outlier: 4.206A pdb=" N ILE B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER B 344 " --> pdb=" O HIS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 398 515 hydrogen bonds defined for protein. 1545 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: 1.77 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2010 1.34 - 1.46: 1360 1.46 - 1.58: 3004 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6434 Sorted by residual: bond pdb=" CB THR A 168 " pdb=" CG2 THR A 168 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.57e+00 bond pdb=" CB THR B 168 " pdb=" CG2 THR B 168 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.57e+00 bond pdb=" CB MET A 377 " pdb=" CG MET A 377 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.15e-01 bond pdb=" CB MET B 377 " pdb=" CG MET B 377 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.15e-01 bond pdb=" CB THR B 73 " pdb=" CG2 THR B 73 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.82e-01 ... (remaining 6429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 8260 1.13 - 2.27: 370 2.27 - 3.40: 44 3.40 - 4.54: 10 4.54 - 5.67: 8 Bond angle restraints: 8692 Sorted by residual: angle pdb=" C VAL A 105 " pdb=" N GLU A 106 " pdb=" CA GLU A 106 " ideal model delta sigma weight residual 119.78 122.06 -2.28 1.24e+00 6.50e-01 3.37e+00 angle pdb=" C VAL B 105 " pdb=" N GLU B 106 " pdb=" CA GLU B 106 " ideal model delta sigma weight residual 119.78 122.06 -2.28 1.24e+00 6.50e-01 3.37e+00 angle pdb=" N GLU A 307 " pdb=" CA GLU A 307 " pdb=" C GLU A 307 " ideal model delta sigma weight residual 111.11 113.15 -2.04 1.20e+00 6.94e-01 2.88e+00 angle pdb=" N GLU B 307 " pdb=" CA GLU B 307 " pdb=" C GLU B 307 " ideal model delta sigma weight residual 111.11 113.15 -2.04 1.20e+00 6.94e-01 2.88e+00 angle pdb=" C PHE B 182 " pdb=" N VAL B 183 " pdb=" CA VAL B 183 " ideal model delta sigma weight residual 121.97 119.01 2.96 1.80e+00 3.09e-01 2.70e+00 ... (remaining 8687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 3366 16.81 - 33.61: 404 33.61 - 50.42: 74 50.42 - 67.23: 2 67.23 - 84.03: 10 Dihedral angle restraints: 3856 sinusoidal: 1532 harmonic: 2324 Sorted by residual: dihedral pdb=" CA HIS B 259 " pdb=" C HIS B 259 " pdb=" N GLY B 260 " pdb=" CA GLY B 260 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA HIS A 259 " pdb=" C HIS A 259 " pdb=" N GLY A 260 " pdb=" CA GLY A 260 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CB GLU B 307 " pdb=" CG GLU B 307 " pdb=" CD GLU B 307 " pdb=" OE1 GLU B 307 " ideal model delta sinusoidal sigma weight residual 0.00 84.03 -84.03 1 3.00e+01 1.11e-03 9.56e+00 ... (remaining 3853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 516 0.027 - 0.054: 346 0.054 - 0.081: 98 0.081 - 0.108: 20 0.108 - 0.135: 16 Chirality restraints: 996 Sorted by residual: chirality pdb=" CA THR A 308 " pdb=" N THR A 308 " pdb=" C THR A 308 " pdb=" CB THR A 308 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA THR B 308 " pdb=" N THR B 308 " pdb=" C THR B 308 " pdb=" CB THR B 308 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE A 298 " pdb=" N ILE A 298 " pdb=" C ILE A 298 " pdb=" CB ILE A 298 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 993 not shown) Planarity restraints: 1090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 364 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO A 365 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 364 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO B 365 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 365 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 365 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 257 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO A 258 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " 0.019 5.00e-02 4.00e+02 ... (remaining 1087 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 42 2.63 - 3.20: 5928 3.20 - 3.76: 9359 3.76 - 4.33: 12910 4.33 - 4.90: 21301 Nonbonded interactions: 49540 Sorted by model distance: nonbonded pdb=" OH TYR A 291 " pdb=" OG SER B 376 " model vdw 2.061 3.040 nonbonded pdb=" OG SER A 376 " pdb=" OH TYR B 291 " model vdw 2.061 3.040 nonbonded pdb=" OE1 GLU B 213 " pdb=" ND2 ASN B 232 " model vdw 2.284 3.120 nonbonded pdb=" OE1 GLU A 213 " pdb=" ND2 ASN A 232 " model vdw 2.284 3.120 nonbonded pdb=" O SER A 294 " pdb=" NE2 GLN A 297 " model vdw 2.316 3.120 ... (remaining 49535 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.240 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 0.005 0.053 6434 Z= 0.332 Angle : 0.550 5.673 8692 Z= 0.316 Chirality : 0.039 0.135 996 Planarity : 0.004 0.037 1090 Dihedral : 14.665 84.030 2352 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % 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: -0.93 (0.28), residues: 792 helix: 0.06 (0.18), residues: 642 sheet: None (None), residues: 0 loop : -3.31 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 129 HIS 0.003 0.001 HIS A 259 PHE 0.012 0.001 PHE A 200 TYR 0.012 0.001 TYR B 291 ARG 0.002 0.000 ARG B 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.740 Fit side-chains REVERT: A 50 TYR cc_start: 0.7738 (t80) cc_final: 0.7338 (t80) REVERT: A 229 ARG cc_start: 0.6960 (mmt90) cc_final: 0.6567 (ttp80) REVERT: A 261 GLN cc_start: 0.7859 (tp-100) cc_final: 0.7021 (tt0) REVERT: A 387 LYS cc_start: 0.7991 (mttt) cc_final: 0.7667 (mptt) REVERT: B 229 ARG cc_start: 0.6964 (mmt90) cc_final: 0.6578 (ttp80) REVERT: B 261 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7002 (tt0) REVERT: B 387 LYS cc_start: 0.8007 (mttt) cc_final: 0.7690 (mptt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2267 time to fit residues: 36.0268 Evaluate side-chains 92 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 96 GLN A 251 ASN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN A 361 ASN B 54 ASN B 96 GLN B 251 ASN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN B 361 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.158437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117854 restraints weight = 7398.456| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.01 r_work: 0.3195 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6434 Z= 0.235 Angle : 0.529 5.874 8692 Z= 0.281 Chirality : 0.039 0.129 996 Planarity : 0.004 0.044 1090 Dihedral : 4.094 19.532 858 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.72 % Allowed : 8.76 % Favored : 89.51 % 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: 1.31 (0.30), residues: 792 helix: 1.62 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -2.57 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 129 HIS 0.002 0.001 HIS B 259 PHE 0.014 0.001 PHE A 206 TYR 0.013 0.001 TYR B 236 ARG 0.004 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.734 Fit side-chains REVERT: A 67 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8408 (mm-30) REVERT: A 229 ARG cc_start: 0.6992 (mmt90) cc_final: 0.6376 (ttp80) REVERT: A 230 LYS cc_start: 0.8427 (tptt) cc_final: 0.7903 (tttt) REVERT: A 261 GLN cc_start: 0.8330 (tp-100) cc_final: 0.7256 (tt0) REVERT: A 291 TYR cc_start: 0.7518 (m-80) cc_final: 0.7229 (m-10) REVERT: A 297 GLN cc_start: 0.7947 (mm110) cc_final: 0.7632 (mm110) REVERT: A 387 LYS cc_start: 0.7915 (mttt) cc_final: 0.7500 (mptt) REVERT: B 67 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8384 (mm-30) REVERT: B 229 ARG cc_start: 0.7012 (mmt90) cc_final: 0.6376 (ttp80) REVERT: B 230 LYS cc_start: 0.8435 (tptt) cc_final: 0.7914 (tttt) REVERT: B 261 GLN cc_start: 0.8316 (tp-100) cc_final: 0.7239 (tt0) REVERT: B 291 TYR cc_start: 0.7510 (m-80) cc_final: 0.7220 (m-10) REVERT: B 297 GLN cc_start: 0.7951 (mm110) cc_final: 0.7630 (mm110) REVERT: B 387 LYS cc_start: 0.7970 (mttt) cc_final: 0.7533 (mptt) outliers start: 12 outliers final: 8 residues processed: 118 average time/residue: 0.2157 time to fit residues: 32.6149 Evaluate side-chains 99 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 44 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.158243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.117313 restraints weight = 7448.256| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.04 r_work: 0.3212 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6434 Z= 0.228 Angle : 0.509 5.806 8692 Z= 0.272 Chirality : 0.038 0.131 996 Planarity : 0.004 0.046 1090 Dihedral : 3.980 19.590 858 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.44 % Allowed : 12.50 % Favored : 85.06 % 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: 1.94 (0.31), residues: 792 helix: 2.10 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.91 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.002 0.001 HIS B 259 PHE 0.015 0.001 PHE B 206 TYR 0.010 0.001 TYR B 39 ARG 0.001 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.728 Fit side-chains REVERT: A 387 LYS cc_start: 0.7970 (mttt) cc_final: 0.7553 (mptt) REVERT: B 229 ARG cc_start: 0.7046 (mmt90) cc_final: 0.6672 (mmt180) REVERT: B 387 LYS cc_start: 0.7978 (mttt) cc_final: 0.7566 (mptt) outliers start: 17 outliers final: 10 residues processed: 97 average time/residue: 0.2088 time to fit residues: 26.3395 Evaluate side-chains 88 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 13 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** 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 = 0.3853 r_free = 0.3853 target = 0.162304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121564 restraints weight = 7500.819| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.04 r_work: 0.3260 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6434 Z= 0.168 Angle : 0.480 6.259 8692 Z= 0.254 Chirality : 0.037 0.128 996 Planarity : 0.004 0.045 1090 Dihedral : 3.820 17.337 858 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.30 % Allowed : 13.94 % Favored : 83.76 % 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: 2.51 (0.31), residues: 792 helix: 2.50 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.75 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 PHE 0.014 0.001 PHE A 206 TYR 0.010 0.001 TYR B 39 ARG 0.002 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.796 Fit side-chains REVERT: A 230 LYS cc_start: 0.8375 (tptt) cc_final: 0.7916 (tptt) REVERT: A 261 GLN cc_start: 0.8348 (tp-100) cc_final: 0.7399 (tt0) REVERT: A 387 LYS cc_start: 0.7948 (mttt) cc_final: 0.7537 (mptt) REVERT: B 229 ARG cc_start: 0.7031 (mmt90) cc_final: 0.6667 (mmt180) REVERT: B 230 LYS cc_start: 0.8385 (tptt) cc_final: 0.7930 (tptt) REVERT: B 261 GLN cc_start: 0.8350 (tp-100) cc_final: 0.7388 (tt0) REVERT: B 387 LYS cc_start: 0.7965 (mttt) cc_final: 0.7545 (mptt) outliers start: 16 outliers final: 12 residues processed: 103 average time/residue: 0.1931 time to fit residues: 26.1277 Evaluate side-chains 98 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 285 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.159888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118456 restraints weight = 7505.140| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.05 r_work: 0.3247 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6434 Z= 0.196 Angle : 0.512 7.598 8692 Z= 0.265 Chirality : 0.038 0.135 996 Planarity : 0.004 0.045 1090 Dihedral : 3.808 17.454 858 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.30 % Allowed : 15.37 % Favored : 82.33 % 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: 2.70 (0.31), residues: 792 helix: 2.62 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.65 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 255 HIS 0.003 0.001 HIS B 259 PHE 0.015 0.001 PHE A 206 TYR 0.010 0.001 TYR B 39 ARG 0.002 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.603 Fit side-chains REVERT: A 230 LYS cc_start: 0.8450 (tptt) cc_final: 0.8003 (tptt) REVERT: A 261 GLN cc_start: 0.8394 (tp-100) cc_final: 0.7505 (tt0) REVERT: A 387 LYS cc_start: 0.8006 (mttt) cc_final: 0.7588 (mptt) REVERT: B 229 ARG cc_start: 0.7069 (mmt90) cc_final: 0.6734 (mmt180) REVERT: B 230 LYS cc_start: 0.8459 (tptt) cc_final: 0.8015 (tptt) REVERT: B 261 GLN cc_start: 0.8406 (tp-100) cc_final: 0.7499 (tt0) REVERT: B 387 LYS cc_start: 0.7996 (mttt) cc_final: 0.7585 (mptt) outliers start: 16 outliers final: 11 residues processed: 96 average time/residue: 0.1962 time to fit residues: 24.7052 Evaluate side-chains 88 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 285 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 19 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.162984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121929 restraints weight = 7463.282| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.04 r_work: 0.3269 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6434 Z= 0.175 Angle : 0.491 7.083 8692 Z= 0.254 Chirality : 0.037 0.127 996 Planarity : 0.004 0.046 1090 Dihedral : 3.758 16.515 858 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.87 % Allowed : 15.80 % Favored : 81.32 % 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: 2.90 (0.31), residues: 792 helix: 2.76 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.64 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 129 HIS 0.003 0.001 HIS B 259 PHE 0.013 0.001 PHE B 206 TYR 0.008 0.001 TYR B 39 ARG 0.001 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.687 Fit side-chains REVERT: A 230 LYS cc_start: 0.8450 (tptt) cc_final: 0.8044 (tptt) REVERT: A 261 GLN cc_start: 0.8362 (tp-100) cc_final: 0.7498 (tt0) REVERT: A 297 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7886 (mm110) REVERT: A 322 LYS cc_start: 0.8239 (tttm) cc_final: 0.7968 (tppt) REVERT: A 387 LYS cc_start: 0.7980 (mttt) cc_final: 0.7540 (mptt) REVERT: B 229 ARG cc_start: 0.7032 (mmt90) cc_final: 0.6722 (mmt180) REVERT: B 230 LYS cc_start: 0.8493 (tptt) cc_final: 0.8109 (tptt) REVERT: B 261 GLN cc_start: 0.8373 (tp-100) cc_final: 0.7493 (tt0) REVERT: B 297 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7757 (mm110) REVERT: B 322 LYS cc_start: 0.8229 (tttm) cc_final: 0.7924 (tppt) REVERT: B 387 LYS cc_start: 0.7986 (mttt) cc_final: 0.7550 (mptt) outliers start: 20 outliers final: 16 residues processed: 106 average time/residue: 0.1975 time to fit residues: 27.6537 Evaluate side-chains 103 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 359 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.159934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118559 restraints weight = 7416.551| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.04 r_work: 0.3247 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6434 Z= 0.205 Angle : 0.518 7.141 8692 Z= 0.269 Chirality : 0.037 0.133 996 Planarity : 0.004 0.046 1090 Dihedral : 3.775 16.982 858 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.30 % Allowed : 16.24 % Favored : 80.46 % 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: 2.90 (0.31), residues: 792 helix: 2.76 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.58 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 255 HIS 0.003 0.001 HIS B 259 PHE 0.014 0.001 PHE B 206 TYR 0.009 0.001 TYR B 39 ARG 0.001 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.721 Fit side-chains REVERT: A 213 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7847 (tt0) REVERT: A 230 LYS cc_start: 0.8521 (tptt) cc_final: 0.8131 (tptt) REVERT: A 261 GLN cc_start: 0.8369 (tp-100) cc_final: 0.7500 (tt0) REVERT: A 322 LYS cc_start: 0.8265 (tttm) cc_final: 0.7980 (tppt) REVERT: A 387 LYS cc_start: 0.8026 (mttt) cc_final: 0.7593 (mptt) REVERT: B 213 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7843 (tt0) REVERT: B 229 ARG cc_start: 0.7056 (mmt90) cc_final: 0.6759 (mmt180) REVERT: B 230 LYS cc_start: 0.8526 (tptt) cc_final: 0.8144 (tptt) REVERT: B 261 GLN cc_start: 0.8375 (tp-100) cc_final: 0.7496 (tt0) REVERT: B 322 LYS cc_start: 0.8280 (tttm) cc_final: 0.7987 (tppt) REVERT: B 387 LYS cc_start: 0.8050 (mttt) cc_final: 0.7613 (mptt) outliers start: 23 outliers final: 17 residues processed: 105 average time/residue: 0.1921 time to fit residues: 26.6028 Evaluate side-chains 104 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 359 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN B 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.160219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.118861 restraints weight = 7475.807| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.04 r_work: 0.3250 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6434 Z= 0.192 Angle : 0.510 7.097 8692 Z= 0.264 Chirality : 0.037 0.134 996 Planarity : 0.004 0.046 1090 Dihedral : 3.752 16.817 858 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.87 % Allowed : 17.10 % Favored : 80.03 % 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: 2.99 (0.31), residues: 792 helix: 2.83 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.60 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 129 HIS 0.003 0.001 HIS B 259 PHE 0.014 0.001 PHE B 206 TYR 0.009 0.001 TYR B 39 ARG 0.001 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.685 Fit side-chains REVERT: A 41 TYR cc_start: 0.6904 (m-80) cc_final: 0.6484 (m-10) REVERT: A 230 LYS cc_start: 0.8502 (tptt) cc_final: 0.8129 (tptt) REVERT: A 261 GLN cc_start: 0.8384 (tp-100) cc_final: 0.7562 (tt0) REVERT: A 322 LYS cc_start: 0.8250 (tttm) cc_final: 0.7957 (tppt) REVERT: A 387 LYS cc_start: 0.8047 (mttt) cc_final: 0.7615 (mptt) REVERT: B 41 TYR cc_start: 0.6871 (m-80) cc_final: 0.6483 (m-10) REVERT: B 50 TYR cc_start: 0.8014 (t80) cc_final: 0.7801 (t80) REVERT: B 230 LYS cc_start: 0.8505 (tptt) cc_final: 0.8136 (tptt) REVERT: B 261 GLN cc_start: 0.8399 (tp-100) cc_final: 0.7561 (tt0) REVERT: B 297 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7646 (mm110) REVERT: B 322 LYS cc_start: 0.8256 (tttm) cc_final: 0.7957 (tppt) REVERT: B 387 LYS cc_start: 0.8064 (mttt) cc_final: 0.7616 (mptt) outliers start: 20 outliers final: 19 residues processed: 105 average time/residue: 0.1882 time to fit residues: 26.0261 Evaluate side-chains 102 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.162025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120688 restraints weight = 7510.852| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.04 r_work: 0.3243 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6434 Z= 0.177 Angle : 0.519 7.186 8692 Z= 0.268 Chirality : 0.037 0.131 996 Planarity : 0.004 0.047 1090 Dihedral : 3.711 16.317 858 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.59 % Allowed : 18.10 % Favored : 79.31 % 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: 3.05 (0.31), residues: 792 helix: 2.87 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.58 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.003 0.001 HIS B 259 PHE 0.013 0.001 PHE B 206 TYR 0.008 0.001 TYR A 39 ARG 0.002 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.678 Fit side-chains REVERT: A 41 TYR cc_start: 0.6811 (m-80) cc_final: 0.6390 (m-10) REVERT: A 230 LYS cc_start: 0.8461 (tptt) cc_final: 0.8089 (tttt) REVERT: A 261 GLN cc_start: 0.8375 (tp-100) cc_final: 0.7555 (tt0) REVERT: A 297 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7992 (mm110) REVERT: A 322 LYS cc_start: 0.8190 (tttm) cc_final: 0.7869 (tppt) REVERT: A 368 MET cc_start: 0.8315 (tpp) cc_final: 0.8057 (tpp) REVERT: A 387 LYS cc_start: 0.7977 (mttt) cc_final: 0.7530 (mptt) REVERT: B 41 TYR cc_start: 0.6811 (m-80) cc_final: 0.6381 (m-10) REVERT: B 50 TYR cc_start: 0.8022 (t80) cc_final: 0.7774 (t80) REVERT: B 230 LYS cc_start: 0.8471 (tptt) cc_final: 0.8104 (tttt) REVERT: B 261 GLN cc_start: 0.8387 (tp-100) cc_final: 0.7556 (tt0) REVERT: B 322 LYS cc_start: 0.8197 (tttm) cc_final: 0.7867 (tppt) REVERT: B 387 LYS cc_start: 0.8010 (mttt) cc_final: 0.7555 (mptt) outliers start: 18 outliers final: 16 residues processed: 100 average time/residue: 0.1882 time to fit residues: 25.0160 Evaluate side-chains 110 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 359 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 68 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.160754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119265 restraints weight = 7553.740| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.05 r_work: 0.3227 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6434 Z= 0.197 Angle : 0.532 7.620 8692 Z= 0.274 Chirality : 0.037 0.131 996 Planarity : 0.004 0.047 1090 Dihedral : 3.741 16.405 858 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.73 % Allowed : 18.10 % Favored : 79.17 % 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: 2.99 (0.31), residues: 792 helix: 2.83 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.60 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 PHE 0.014 0.001 PHE B 206 TYR 0.014 0.001 TYR A 50 ARG 0.002 0.000 ARG B 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.710 Fit side-chains REVERT: A 230 LYS cc_start: 0.8458 (tptt) cc_final: 0.8076 (tttt) REVERT: A 261 GLN cc_start: 0.8351 (tp-100) cc_final: 0.7555 (tt0) REVERT: A 322 LYS cc_start: 0.8193 (tttm) cc_final: 0.7875 (tppt) REVERT: A 324 MET cc_start: 0.7892 (ttm) cc_final: 0.7586 (ttm) REVERT: A 387 LYS cc_start: 0.7932 (mttt) cc_final: 0.7532 (mptt) REVERT: B 41 TYR cc_start: 0.6789 (m-80) cc_final: 0.5768 (m-80) REVERT: B 50 TYR cc_start: 0.8074 (t80) cc_final: 0.7819 (t80) REVERT: B 213 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7571 (tt0) REVERT: B 230 LYS cc_start: 0.8472 (tptt) cc_final: 0.8095 (tttt) REVERT: B 261 GLN cc_start: 0.8361 (tp-100) cc_final: 0.7554 (tt0) REVERT: B 322 LYS cc_start: 0.8201 (tttm) cc_final: 0.7876 (tppt) REVERT: B 324 MET cc_start: 0.7889 (ttm) cc_final: 0.7579 (ttm) REVERT: B 387 LYS cc_start: 0.7963 (mttt) cc_final: 0.7549 (mptt) outliers start: 19 outliers final: 17 residues processed: 112 average time/residue: 0.1907 time to fit residues: 28.4374 Evaluate side-chains 114 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 359 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.160625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.119072 restraints weight = 7647.412| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.06 r_work: 0.3229 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6434 Z= 0.198 Angle : 0.533 7.313 8692 Z= 0.275 Chirality : 0.037 0.131 996 Planarity : 0.004 0.048 1090 Dihedral : 3.739 16.648 858 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.44 % Allowed : 18.68 % Favored : 78.88 % 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: 2.99 (0.31), residues: 792 helix: 2.83 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.60 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 PHE 0.014 0.001 PHE B 206 TYR 0.025 0.001 TYR A 236 ARG 0.002 0.000 ARG B 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3303.04 seconds wall clock time: 59 minutes 12.04 seconds (3552.04 seconds total)