Starting phenix.real_space_refine on Sat Jan 18 05:47:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x82_38133/01_2025/8x82_38133_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x82_38133/01_2025/8x82_38133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x82_38133/01_2025/8x82_38133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x82_38133/01_2025/8x82_38133.map" model { file = "/net/cci-nas-00/data/ceres_data/8x82_38133/01_2025/8x82_38133_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x82_38133/01_2025/8x82_38133_neut.cif" } resolution = 2.8 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= 0.006 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 72 5.16 5 C 7796 2.51 5 N 2048 2.21 5 O 2088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 12004 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3001 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 6, 'TRANS': 373} Chain breaks: 1 Restraints were copied for chains: C, B, D Time building chain proxies: 6.11, per 1000 atoms: 0.51 Number of scatterers: 12004 At special positions: 0 Unit cell: (108.81, 108.81, 105.09, 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 72 16.00 O 2088 8.00 N 2048 7.00 C 7796 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: 3.06 Conformation dependent library (CDL) restraints added in 1.5 seconds 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 85.3% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 Processing helix chain 'A' and resid 37 through 64 Processing helix chain 'A' and resid 73 through 100 removed outlier: 3.603A pdb=" N VAL A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 119 Processing helix chain 'A' and resid 120 through 123 removed outlier: 3.539A pdb=" N ASN A 123 " --> pdb=" O ASN A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 124 through 162 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.534A pdb=" N VAL A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 215 Processing helix chain 'A' and resid 263 through 321 removed outlier: 6.049A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ALA A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 357 Proline residue: A 347 - end of helix Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 371 through 387 removed outlier: 4.207A pdb=" N VAL A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 425 removed outlier: 3.651A pdb=" N THR A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 17 Processing helix chain 'B' and resid 37 through 64 Processing helix chain 'B' and resid 73 through 100 removed outlier: 3.603A pdb=" N VAL B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 119 Processing helix chain 'B' and resid 120 through 123 removed outlier: 3.539A pdb=" N ASN B 123 " --> pdb=" O ASN B 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 124 through 162 Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.534A pdb=" N VAL B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 215 Processing helix chain 'B' and resid 263 through 321 removed outlier: 6.049A pdb=" N ILE B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ALA B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 357 Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 357 through 369 Processing helix chain 'B' and resid 371 through 387 removed outlier: 4.207A pdb=" N VAL B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 425 removed outlier: 3.652A pdb=" N THR B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 17 Processing helix chain 'C' and resid 37 through 64 Processing helix chain 'C' and resid 73 through 100 removed outlier: 3.603A pdb=" N VAL C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 119 Processing helix chain 'C' and resid 120 through 123 removed outlier: 3.539A pdb=" N ASN C 123 " --> pdb=" O ASN C 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 124 through 162 Processing helix chain 'C' and resid 168 through 174 removed outlier: 3.534A pdb=" N VAL C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 215 Processing helix chain 'C' and resid 263 through 321 removed outlier: 6.049A pdb=" N ILE C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ALA C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 357 Proline residue: C 347 - end of helix Processing helix chain 'C' and resid 357 through 369 Processing helix chain 'C' and resid 371 through 387 removed outlier: 4.207A pdb=" N VAL C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 425 removed outlier: 3.651A pdb=" N THR C 406 " --> pdb=" O ARG C 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 17 Processing helix chain 'D' and resid 37 through 64 Processing helix chain 'D' and resid 73 through 100 removed outlier: 3.603A pdb=" N VAL D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 120 through 123 removed outlier: 3.539A pdb=" N ASN D 123 " --> pdb=" O ASN D 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 124 through 162 Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.534A pdb=" N VAL D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 215 Processing helix chain 'D' and resid 263 through 321 removed outlier: 6.049A pdb=" N ILE D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ALA D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 357 Proline residue: D 347 - end of helix Processing helix chain 'D' and resid 357 through 369 Processing helix chain 'D' and resid 371 through 387 removed outlier: 4.207A pdb=" N VAL D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 425 removed outlier: 3.651A pdb=" N THR D 406 " --> pdb=" O ARG D 402 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 26 removed outlier: 3.527A pdb=" N VAL A 25 " --> pdb=" O GLU A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 393 removed outlier: 4.511A pdb=" N PHE A 392 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 26 removed outlier: 3.527A pdb=" N VAL B 25 " --> pdb=" O GLU B 33 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 392 through 393 removed outlier: 4.511A pdb=" N PHE B 392 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 removed outlier: 3.527A pdb=" N VAL C 25 " --> pdb=" O GLU C 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 392 through 393 removed outlier: 4.511A pdb=" N PHE C 392 " --> pdb=" O VAL C 400 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 26 removed outlier: 3.527A pdb=" N VAL D 25 " --> pdb=" O GLU D 33 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 392 through 393 removed outlier: 4.511A pdb=" N PHE D 392 " --> pdb=" O VAL D 400 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 3204 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: 4.13 Time building geometry restraints manager: 3.54 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: 3790 1.34 - 1.46: 2718 1.46 - 1.58: 5616 1.58 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 12236 Sorted by residual: bond pdb=" CA ILE A 176 " pdb=" C ILE A 176 " ideal model delta sigma weight residual 1.520 1.528 -0.009 8.80e-03 1.29e+04 9.99e-01 bond pdb=" CA ILE B 176 " pdb=" C ILE B 176 " ideal model delta sigma weight residual 1.520 1.528 -0.009 8.80e-03 1.29e+04 9.99e-01 bond pdb=" C ILE B 67 " pdb=" O ILE B 67 " ideal model delta sigma weight residual 1.232 1.240 -0.009 1.01e-02 9.80e+03 7.92e-01 bond pdb=" C ILE D 67 " pdb=" O ILE D 67 " ideal model delta sigma weight residual 1.232 1.240 -0.009 1.01e-02 9.80e+03 7.92e-01 bond pdb=" C ILE D 176 " pdb=" N PRO D 177 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.28e-02 6.10e+03 6.36e-01 ... (remaining 12231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 16165 1.00 - 2.00: 338 2.00 - 3.01: 63 3.01 - 4.01: 18 4.01 - 5.01: 12 Bond angle restraints: 16596 Sorted by residual: angle pdb=" C TYR B 175 " pdb=" N ILE B 176 " pdb=" CA ILE B 176 " ideal model delta sigma weight residual 120.24 123.00 -2.76 6.30e-01 2.52e+00 1.91e+01 angle pdb=" C TYR A 175 " pdb=" N ILE A 176 " pdb=" CA ILE A 176 " ideal model delta sigma weight residual 120.24 123.00 -2.76 6.30e-01 2.52e+00 1.91e+01 angle pdb=" C TYR C 175 " pdb=" N ILE C 176 " pdb=" CA ILE C 176 " ideal model delta sigma weight residual 120.33 123.03 -2.70 8.00e-01 1.56e+00 1.14e+01 angle pdb=" C TYR D 175 " pdb=" N ILE D 176 " pdb=" CA ILE D 176 " ideal model delta sigma weight residual 120.33 123.03 -2.70 8.00e-01 1.56e+00 1.14e+01 angle pdb=" C VAL D 345 " pdb=" N GLU D 346 " pdb=" CA GLU D 346 " ideal model delta sigma weight residual 120.26 124.12 -3.86 1.34e+00 5.57e-01 8.31e+00 ... (remaining 16591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 6284 17.10 - 34.21: 712 34.21 - 51.31: 200 51.31 - 68.42: 32 68.42 - 85.52: 24 Dihedral angle restraints: 7252 sinusoidal: 2792 harmonic: 4460 Sorted by residual: dihedral pdb=" CA ASP B 276 " pdb=" CB ASP B 276 " pdb=" CG ASP B 276 " pdb=" OD1 ASP B 276 " ideal model delta sinusoidal sigma weight residual -30.00 -88.04 58.04 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP D 276 " pdb=" CB ASP D 276 " pdb=" CG ASP D 276 " pdb=" OD1 ASP D 276 " ideal model delta sinusoidal sigma weight residual -30.00 -87.99 57.99 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP A 276 " pdb=" CB ASP A 276 " pdb=" CG ASP A 276 " pdb=" OD1 ASP A 276 " ideal model delta sinusoidal sigma weight residual -30.00 -87.99 57.99 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 7249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1210 0.024 - 0.047: 470 0.047 - 0.071: 244 0.071 - 0.095: 37 0.095 - 0.119: 27 Chirality restraints: 1988 Sorted by residual: chirality pdb=" CA ILE A 163 " pdb=" N ILE A 163 " pdb=" C ILE A 163 " pdb=" CB ILE A 163 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA ILE C 163 " pdb=" N ILE C 163 " pdb=" C ILE C 163 " pdb=" CB ILE C 163 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA ILE D 163 " pdb=" N ILE D 163 " pdb=" C ILE D 163 " pdb=" CB ILE D 163 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 1985 not shown) Planarity restraints: 2032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 176 " 0.017 5.00e-02 4.00e+02 2.52e-02 1.01e+00 pdb=" N PRO B 177 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 177 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 177 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 176 " 0.017 5.00e-02 4.00e+02 2.52e-02 1.01e+00 pdb=" N PRO A 177 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 177 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 177 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 176 " -0.017 5.00e-02 4.00e+02 2.50e-02 1.00e+00 pdb=" N PRO C 177 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO C 177 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 177 " -0.014 5.00e-02 4.00e+02 ... (remaining 2029 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 284 2.72 - 3.27: 12504 3.27 - 3.81: 21460 3.81 - 4.36: 23941 4.36 - 4.90: 42851 Nonbonded interactions: 101040 Sorted by model distance: nonbonded pdb=" O ALA D 81 " pdb=" OG SER D 85 " model vdw 2.181 3.040 nonbonded pdb=" O ALA A 81 " pdb=" OG SER A 85 " model vdw 2.181 3.040 nonbonded pdb=" O ALA C 81 " pdb=" OG SER C 85 " model vdw 2.181 3.040 nonbonded pdb=" O ALA B 81 " pdb=" OG SER B 85 " model vdw 2.181 3.040 nonbonded pdb=" OD1 ASN A 207 " pdb=" OG1 THR A 358 " model vdw 2.244 3.040 ... (remaining 101035 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.810 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.760 Find NCS groups from input model: 0.310 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:13.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 0.025 12236 Z= 0.134 Angle : 0.408 5.012 16596 Z= 0.260 Chirality : 0.033 0.119 1988 Planarity : 0.002 0.025 2032 Dihedral : 16.428 85.523 4356 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.84 % Allowed : 18.12 % Favored : 81.04 % 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: 3.68 (0.21), residues: 1504 helix: 3.02 (0.13), residues: 1248 sheet: 1.67 (0.77), residues: 48 loop : -1.49 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 154 HIS 0.002 0.001 HIS A 306 PHE 0.007 0.001 PHE B 178 TYR 0.005 0.001 TYR B 415 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 1.316 Fit side-chains REVERT: A 126 ARG cc_start: 0.6565 (mmm160) cc_final: 0.5840 (mtm110) REVERT: A 129 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.7061 (ttm170) REVERT: A 131 ARG cc_start: 0.6936 (mpt-90) cc_final: 0.5478 (tmt-80) REVERT: A 272 LYS cc_start: 0.6744 (tppp) cc_final: 0.5990 (ttpp) REVERT: A 279 GLU cc_start: 0.8121 (tt0) cc_final: 0.7790 (tt0) REVERT: A 367 ARG cc_start: 0.6379 (mtm-85) cc_final: 0.6145 (mtm-85) REVERT: A 399 ARG cc_start: 0.7766 (mtm180) cc_final: 0.7120 (tpt170) REVERT: B 126 ARG cc_start: 0.6536 (mmm160) cc_final: 0.5802 (mtm110) REVERT: B 129 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.7064 (ttm170) REVERT: B 131 ARG cc_start: 0.6936 (mpt-90) cc_final: 0.5481 (tmt-80) REVERT: B 272 LYS cc_start: 0.6761 (tppp) cc_final: 0.5993 (ttpp) REVERT: B 279 GLU cc_start: 0.8120 (tt0) cc_final: 0.7791 (tt0) REVERT: B 399 ARG cc_start: 0.7769 (mtm180) cc_final: 0.7140 (tpt170) REVERT: C 126 ARG cc_start: 0.6535 (mmm160) cc_final: 0.5800 (mtm110) REVERT: C 129 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.7064 (ttm170) REVERT: C 131 ARG cc_start: 0.6938 (mpt-90) cc_final: 0.5478 (tmt-80) REVERT: C 272 LYS cc_start: 0.6743 (tppp) cc_final: 0.5988 (ttpp) REVERT: C 279 GLU cc_start: 0.8120 (tt0) cc_final: 0.7791 (tt0) REVERT: C 399 ARG cc_start: 0.7767 (mtm180) cc_final: 0.7175 (tpt170) REVERT: D 126 ARG cc_start: 0.6563 (mmm160) cc_final: 0.5840 (mtm110) REVERT: D 129 ARG cc_start: 0.7395 (ttm-80) cc_final: 0.7061 (ttm170) REVERT: D 131 ARG cc_start: 0.6938 (mpt-90) cc_final: 0.5478 (tmt-80) REVERT: D 272 LYS cc_start: 0.6744 (tppp) cc_final: 0.5985 (ttpp) REVERT: D 279 GLU cc_start: 0.8120 (tt0) cc_final: 0.7716 (tt0) REVERT: D 399 ARG cc_start: 0.7766 (mtm180) cc_final: 0.7137 (tpt170) outliers start: 11 outliers final: 0 residues processed: 191 average time/residue: 1.4844 time to fit residues: 303.8999 Evaluate side-chains 136 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 383 GLN A 421 GLN A 423 GLN B 189 GLN B 383 GLN B 421 GLN B 423 GLN C 189 GLN C 383 GLN C 421 GLN C 423 GLN D 189 GLN D 383 GLN D 421 GLN D 423 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.157725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.112956 restraints weight = 12012.643| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.66 r_work: 0.3037 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12236 Z= 0.311 Angle : 0.507 4.881 16596 Z= 0.276 Chirality : 0.039 0.133 1988 Planarity : 0.004 0.025 2032 Dihedral : 3.548 12.475 1656 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.06 % Allowed : 15.60 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.11 (0.20), residues: 1504 helix: 2.56 (0.13), residues: 1260 sheet: 1.23 (0.76), residues: 48 loop : -1.33 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 130 HIS 0.003 0.001 HIS B 349 PHE 0.013 0.002 PHE C 11 TYR 0.017 0.002 TYR B 175 ARG 0.003 0.001 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 1.272 Fit side-chains REVERT: A 51 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7868 (mmt) REVERT: A 114 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7301 (mtmt) REVERT: A 126 ARG cc_start: 0.7198 (mtm110) cc_final: 0.6429 (mtm110) REVERT: A 131 ARG cc_start: 0.7672 (mpt-90) cc_final: 0.6158 (tmt-80) REVERT: A 272 LYS cc_start: 0.7326 (tppp) cc_final: 0.6701 (ttpp) REVERT: A 279 GLU cc_start: 0.8514 (tt0) cc_final: 0.8246 (tt0) REVERT: A 399 ARG cc_start: 0.8442 (mtm180) cc_final: 0.7592 (tpt170) REVERT: B 51 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7862 (mmt) REVERT: B 114 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7298 (mtmt) REVERT: B 126 ARG cc_start: 0.7202 (mtm110) cc_final: 0.6430 (mtm110) REVERT: B 131 ARG cc_start: 0.7664 (mpt-90) cc_final: 0.6149 (tmt-80) REVERT: B 272 LYS cc_start: 0.7338 (tppp) cc_final: 0.6699 (ttpp) REVERT: B 279 GLU cc_start: 0.8503 (tt0) cc_final: 0.8234 (tt0) REVERT: B 399 ARG cc_start: 0.8446 (mtm180) cc_final: 0.7594 (tpt170) REVERT: C 51 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7861 (mmt) REVERT: C 114 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7317 (mtmt) REVERT: C 126 ARG cc_start: 0.7192 (mtm110) cc_final: 0.6443 (mtm110) REVERT: C 131 ARG cc_start: 0.7676 (mpt-90) cc_final: 0.6163 (tmt-80) REVERT: C 272 LYS cc_start: 0.7331 (tppp) cc_final: 0.6705 (ttpp) REVERT: C 279 GLU cc_start: 0.8501 (tt0) cc_final: 0.8231 (tt0) REVERT: C 399 ARG cc_start: 0.8440 (mtm180) cc_final: 0.7610 (tpt170) REVERT: D 51 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7864 (mmt) REVERT: D 114 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7319 (mtmt) REVERT: D 126 ARG cc_start: 0.7192 (mtm110) cc_final: 0.6421 (mtm110) REVERT: D 131 ARG cc_start: 0.7681 (mpt-90) cc_final: 0.6162 (tmt-80) REVERT: D 272 LYS cc_start: 0.7336 (tppp) cc_final: 0.6710 (ttpp) REVERT: D 279 GLU cc_start: 0.8547 (tt0) cc_final: 0.8338 (tt0) REVERT: D 399 ARG cc_start: 0.8468 (mtm180) cc_final: 0.7643 (tpt170) outliers start: 40 outliers final: 12 residues processed: 172 average time/residue: 1.4654 time to fit residues: 270.8107 Evaluate side-chains 168 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 189 GLN A 383 GLN B 27 ASN B 189 GLN B 383 GLN C 27 ASN C 189 GLN C 383 GLN D 27 ASN D 189 GLN D 383 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.157741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.112619 restraints weight = 12176.161| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.66 r_work: 0.2985 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12236 Z= 0.250 Angle : 0.461 5.276 16596 Z= 0.254 Chirality : 0.037 0.129 1988 Planarity : 0.003 0.025 2032 Dihedral : 3.590 12.780 1656 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.75 % Allowed : 16.74 % Favored : 80.50 % 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: 3.03 (0.21), residues: 1504 helix: 2.50 (0.13), residues: 1264 sheet: 1.15 (0.73), residues: 48 loop : -1.36 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 130 HIS 0.002 0.001 HIS D 337 PHE 0.013 0.002 PHE A 422 TYR 0.011 0.001 TYR B 175 ARG 0.002 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 1.561 Fit side-chains REVERT: A 25 VAL cc_start: 0.8134 (p) cc_final: 0.7925 (m) REVERT: A 71 MET cc_start: 0.7170 (mmm) cc_final: 0.6497 (mmm) REVERT: A 126 ARG cc_start: 0.7244 (mtm110) cc_final: 0.6509 (mtm110) REVERT: A 131 ARG cc_start: 0.7789 (mpt-90) cc_final: 0.6315 (tmt-80) REVERT: A 272 LYS cc_start: 0.7401 (tppp) cc_final: 0.6873 (ttpp) REVERT: A 279 GLU cc_start: 0.8534 (tt0) cc_final: 0.8260 (tt0) REVERT: A 313 PHE cc_start: 0.7010 (OUTLIER) cc_final: 0.6584 (m-10) REVERT: A 331 MET cc_start: 0.7333 (ttp) cc_final: 0.7099 (ttp) REVERT: A 399 ARG cc_start: 0.8497 (mtm180) cc_final: 0.7652 (tpt170) REVERT: A 410 SER cc_start: 0.9251 (OUTLIER) cc_final: 0.8815 (m) REVERT: B 25 VAL cc_start: 0.8133 (p) cc_final: 0.7922 (m) REVERT: B 71 MET cc_start: 0.7166 (mmm) cc_final: 0.6499 (mmm) REVERT: B 126 ARG cc_start: 0.7239 (mtm110) cc_final: 0.6501 (mtm110) REVERT: B 131 ARG cc_start: 0.7789 (mpt-90) cc_final: 0.6315 (tmt-80) REVERT: B 272 LYS cc_start: 0.7396 (tppp) cc_final: 0.6864 (ttpp) REVERT: B 279 GLU cc_start: 0.8524 (tt0) cc_final: 0.8254 (tt0) REVERT: B 313 PHE cc_start: 0.7019 (OUTLIER) cc_final: 0.6595 (m-10) REVERT: B 331 MET cc_start: 0.7371 (ttp) cc_final: 0.7132 (ttp) REVERT: B 399 ARG cc_start: 0.8508 (mtm180) cc_final: 0.7669 (tpt170) REVERT: B 410 SER cc_start: 0.9254 (OUTLIER) cc_final: 0.8818 (m) REVERT: C 25 VAL cc_start: 0.8130 (p) cc_final: 0.7921 (m) REVERT: C 71 MET cc_start: 0.7161 (mmm) cc_final: 0.6485 (mmm) REVERT: C 126 ARG cc_start: 0.7242 (mtm110) cc_final: 0.6502 (mtm110) REVERT: C 131 ARG cc_start: 0.7791 (mpt-90) cc_final: 0.6320 (tmt-80) REVERT: C 272 LYS cc_start: 0.7405 (tppp) cc_final: 0.6875 (ttpp) REVERT: C 279 GLU cc_start: 0.8531 (tt0) cc_final: 0.8260 (tt0) REVERT: C 313 PHE cc_start: 0.7014 (OUTLIER) cc_final: 0.6590 (m-10) REVERT: C 331 MET cc_start: 0.7367 (ttp) cc_final: 0.7127 (ttp) REVERT: C 399 ARG cc_start: 0.8508 (mtm180) cc_final: 0.7667 (tpt170) REVERT: C 410 SER cc_start: 0.9256 (OUTLIER) cc_final: 0.8821 (m) REVERT: D 25 VAL cc_start: 0.8131 (p) cc_final: 0.7924 (m) REVERT: D 71 MET cc_start: 0.7165 (mmm) cc_final: 0.6494 (mmm) REVERT: D 126 ARG cc_start: 0.7224 (mtm110) cc_final: 0.6487 (mtm110) REVERT: D 131 ARG cc_start: 0.7786 (mpt-90) cc_final: 0.6311 (tmt-80) REVERT: D 272 LYS cc_start: 0.7400 (tppp) cc_final: 0.6867 (ttpp) REVERT: D 313 PHE cc_start: 0.7013 (OUTLIER) cc_final: 0.6588 (m-10) REVERT: D 331 MET cc_start: 0.7343 (ttp) cc_final: 0.7107 (ttp) REVERT: D 399 ARG cc_start: 0.8509 (mtm180) cc_final: 0.7665 (tpt170) REVERT: D 410 SER cc_start: 0.9253 (OUTLIER) cc_final: 0.8817 (m) outliers start: 36 outliers final: 12 residues processed: 163 average time/residue: 1.2287 time to fit residues: 218.2839 Evaluate side-chains 155 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 313 PHE Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 53 optimal weight: 1.9990 chunk 149 optimal weight: 0.3980 chunk 85 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 131 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 383 GLN C 383 GLN D 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.160503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.117500 restraints weight = 12053.708| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.54 r_work: 0.3096 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12236 Z= 0.148 Angle : 0.396 4.825 16596 Z= 0.221 Chirality : 0.034 0.131 1988 Planarity : 0.003 0.027 2032 Dihedral : 3.422 12.328 1656 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.83 % Allowed : 17.20 % Favored : 80.96 % 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: 3.48 (0.21), residues: 1504 helix: 2.81 (0.13), residues: 1264 sheet: 1.31 (0.71), residues: 48 loop : -1.24 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 154 HIS 0.001 0.000 HIS C 349 PHE 0.010 0.001 PHE A 11 TYR 0.006 0.001 TYR A 175 ARG 0.002 0.000 ARG C 367 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 1.358 Fit side-chains REVERT: A 51 MET cc_start: 0.8099 (mmt) cc_final: 0.7795 (tpp) REVERT: A 126 ARG cc_start: 0.7068 (mtm110) cc_final: 0.6340 (mtm110) REVERT: A 129 ARG cc_start: 0.7880 (ttm-80) cc_final: 0.7415 (ttm170) REVERT: A 131 ARG cc_start: 0.7616 (tpt-90) cc_final: 0.6060 (ttt180) REVERT: A 173 HIS cc_start: 0.6443 (OUTLIER) cc_final: 0.5533 (m-70) REVERT: A 272 LYS cc_start: 0.7320 (tppp) cc_final: 0.6799 (ttpp) REVERT: A 279 GLU cc_start: 0.8374 (tt0) cc_final: 0.8036 (tt0) REVERT: A 331 MET cc_start: 0.7103 (ttp) cc_final: 0.6862 (ttp) REVERT: A 364 GLU cc_start: 0.7238 (mt-10) cc_final: 0.7037 (mm-30) REVERT: A 380 LYS cc_start: 0.7349 (mmtp) cc_final: 0.6930 (mmmt) REVERT: A 399 ARG cc_start: 0.8339 (mtm180) cc_final: 0.7485 (tpt170) REVERT: B 126 ARG cc_start: 0.7096 (mtm110) cc_final: 0.6368 (mtm110) REVERT: B 129 ARG cc_start: 0.7891 (ttm-80) cc_final: 0.7427 (ttm170) REVERT: B 131 ARG cc_start: 0.7618 (tpt-90) cc_final: 0.6059 (ttt180) REVERT: B 173 HIS cc_start: 0.6417 (OUTLIER) cc_final: 0.5509 (m-70) REVERT: B 272 LYS cc_start: 0.7277 (tppp) cc_final: 0.6761 (ttpp) REVERT: B 279 GLU cc_start: 0.8344 (tt0) cc_final: 0.8003 (tt0) REVERT: B 380 LYS cc_start: 0.7354 (mmtp) cc_final: 0.6932 (mmmt) REVERT: B 399 ARG cc_start: 0.8354 (mtm180) cc_final: 0.7503 (tpt170) REVERT: C 126 ARG cc_start: 0.7081 (mtm110) cc_final: 0.6362 (mtm110) REVERT: C 129 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7409 (ttm170) REVERT: C 131 ARG cc_start: 0.7613 (tpt-90) cc_final: 0.6058 (ttt180) REVERT: C 173 HIS cc_start: 0.6436 (OUTLIER) cc_final: 0.5530 (m-70) REVERT: C 272 LYS cc_start: 0.7311 (tppp) cc_final: 0.6796 (ttpp) REVERT: C 279 GLU cc_start: 0.8372 (tt0) cc_final: 0.8033 (tt0) REVERT: C 380 LYS cc_start: 0.7352 (mmtp) cc_final: 0.6934 (mmmt) REVERT: C 399 ARG cc_start: 0.8346 (mtm180) cc_final: 0.7488 (tpt170) REVERT: D 51 MET cc_start: 0.8088 (mmt) cc_final: 0.7784 (tpp) REVERT: D 126 ARG cc_start: 0.7060 (mtm110) cc_final: 0.6328 (mtm110) REVERT: D 129 ARG cc_start: 0.7861 (ttm-80) cc_final: 0.7390 (ttm170) REVERT: D 131 ARG cc_start: 0.7606 (tpt-90) cc_final: 0.6043 (ttt180) REVERT: D 173 HIS cc_start: 0.6441 (OUTLIER) cc_final: 0.5526 (m-70) REVERT: D 272 LYS cc_start: 0.7309 (tppp) cc_final: 0.6793 (ttpp) REVERT: D 331 MET cc_start: 0.7124 (ttp) cc_final: 0.6883 (ttp) REVERT: D 380 LYS cc_start: 0.7351 (mmtp) cc_final: 0.6936 (mmmt) REVERT: D 399 ARG cc_start: 0.8355 (mtm180) cc_final: 0.7511 (tpt170) outliers start: 24 outliers final: 4 residues processed: 173 average time/residue: 1.4256 time to fit residues: 266.1817 Evaluate side-chains 164 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 404 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 92 optimal weight: 0.0980 chunk 123 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 383 GLN C 383 GLN D 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.159578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.116493 restraints weight = 12035.970| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.54 r_work: 0.3041 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12236 Z= 0.173 Angle : 0.407 4.861 16596 Z= 0.226 Chirality : 0.034 0.131 1988 Planarity : 0.003 0.026 2032 Dihedral : 3.400 11.892 1656 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.83 % Allowed : 19.27 % Favored : 78.90 % 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: 3.51 (0.21), residues: 1504 helix: 2.83 (0.13), residues: 1264 sheet: 1.29 (0.65), residues: 48 loop : -1.23 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 154 HIS 0.001 0.000 HIS C 337 PHE 0.009 0.001 PHE B 11 TYR 0.008 0.001 TYR A 175 ARG 0.002 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 1.269 Fit side-chains REVERT: A 51 MET cc_start: 0.8212 (mmt) cc_final: 0.7880 (tpp) REVERT: A 126 ARG cc_start: 0.7146 (mtm110) cc_final: 0.6382 (mtm110) REVERT: A 131 ARG cc_start: 0.7688 (tpt-90) cc_final: 0.6113 (tmt-80) REVERT: A 173 HIS cc_start: 0.6517 (OUTLIER) cc_final: 0.5584 (m-70) REVERT: A 272 LYS cc_start: 0.7332 (tppp) cc_final: 0.6832 (ttpp) REVERT: A 279 GLU cc_start: 0.8389 (tt0) cc_final: 0.8152 (tt0) REVERT: A 331 MET cc_start: 0.7184 (ttp) cc_final: 0.6946 (ttp) REVERT: A 364 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7097 (mm-30) REVERT: A 380 LYS cc_start: 0.7403 (mmtp) cc_final: 0.6984 (mmmt) REVERT: A 399 ARG cc_start: 0.8411 (mtm180) cc_final: 0.7569 (tpt170) REVERT: B 126 ARG cc_start: 0.7159 (mtm110) cc_final: 0.6395 (mtm110) REVERT: B 131 ARG cc_start: 0.7693 (tpt-90) cc_final: 0.6119 (tmt-80) REVERT: B 173 HIS cc_start: 0.6528 (OUTLIER) cc_final: 0.5605 (m-70) REVERT: B 272 LYS cc_start: 0.7330 (tppp) cc_final: 0.6823 (ttpp) REVERT: B 279 GLU cc_start: 0.8374 (tt0) cc_final: 0.8138 (tt0) REVERT: B 380 LYS cc_start: 0.7415 (mmtp) cc_final: 0.6994 (mmmt) REVERT: B 399 ARG cc_start: 0.8422 (mtm180) cc_final: 0.7583 (tpt170) REVERT: C 126 ARG cc_start: 0.7134 (mtm110) cc_final: 0.6391 (mtm110) REVERT: C 131 ARG cc_start: 0.7704 (tpt-90) cc_final: 0.6125 (tmt-80) REVERT: C 173 HIS cc_start: 0.6521 (OUTLIER) cc_final: 0.5596 (m-70) REVERT: C 272 LYS cc_start: 0.7336 (tppp) cc_final: 0.6829 (ttpp) REVERT: C 279 GLU cc_start: 0.8383 (tt0) cc_final: 0.8145 (tt0) REVERT: C 380 LYS cc_start: 0.7394 (mmtp) cc_final: 0.6975 (mmmt) REVERT: C 399 ARG cc_start: 0.8421 (mtm180) cc_final: 0.7581 (tpt170) REVERT: D 51 MET cc_start: 0.8203 (mmt) cc_final: 0.7873 (tpp) REVERT: D 126 ARG cc_start: 0.7132 (mtm110) cc_final: 0.6370 (mtm110) REVERT: D 131 ARG cc_start: 0.7697 (tpt-90) cc_final: 0.6119 (tmt-80) REVERT: D 173 HIS cc_start: 0.6522 (OUTLIER) cc_final: 0.5598 (m-70) REVERT: D 272 LYS cc_start: 0.7334 (tppp) cc_final: 0.6828 (ttpp) REVERT: D 331 MET cc_start: 0.7192 (ttp) cc_final: 0.6955 (ttp) REVERT: D 380 LYS cc_start: 0.7394 (mmtp) cc_final: 0.6980 (mmmt) REVERT: D 399 ARG cc_start: 0.8418 (mtm180) cc_final: 0.7592 (tpt170) outliers start: 24 outliers final: 5 residues processed: 166 average time/residue: 1.3885 time to fit residues: 249.2430 Evaluate side-chains 159 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 404 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 383 GLN C 383 GLN D 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.157542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.114475 restraints weight = 12187.183| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.54 r_work: 0.3015 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12236 Z= 0.231 Angle : 0.443 5.174 16596 Z= 0.244 Chirality : 0.036 0.130 1988 Planarity : 0.003 0.026 2032 Dihedral : 3.503 12.270 1656 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.06 % Allowed : 17.81 % Favored : 79.13 % 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: 3.29 (0.21), residues: 1504 helix: 2.70 (0.13), residues: 1264 sheet: 0.98 (0.62), residues: 48 loop : -1.40 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 174 HIS 0.002 0.001 HIS B 337 PHE 0.010 0.002 PHE D 11 TYR 0.010 0.001 TYR B 175 ARG 0.003 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 1.304 Fit side-chains REVERT: A 51 MET cc_start: 0.8225 (mmt) cc_final: 0.7893 (tpp) REVERT: A 126 ARG cc_start: 0.7205 (mtm110) cc_final: 0.6405 (mtm110) REVERT: A 131 ARG cc_start: 0.7715 (tpt-90) cc_final: 0.6136 (tmt-80) REVERT: A 272 LYS cc_start: 0.7325 (tppp) cc_final: 0.6799 (ttpp) REVERT: A 279 GLU cc_start: 0.8446 (tt0) cc_final: 0.8127 (tt0) REVERT: A 331 MET cc_start: 0.7170 (ttp) cc_final: 0.6930 (ttp) REVERT: A 364 GLU cc_start: 0.7324 (mt-10) cc_final: 0.7096 (mm-30) REVERT: A 380 LYS cc_start: 0.7442 (mmtp) cc_final: 0.6990 (mmmt) REVERT: A 399 ARG cc_start: 0.8463 (mtm180) cc_final: 0.7617 (tpt170) REVERT: A 410 SER cc_start: 0.9204 (OUTLIER) cc_final: 0.8745 (m) REVERT: B 126 ARG cc_start: 0.7210 (mtm110) cc_final: 0.6415 (mtm110) REVERT: B 131 ARG cc_start: 0.7716 (tpt-90) cc_final: 0.6159 (tmt-80) REVERT: B 272 LYS cc_start: 0.7304 (tppp) cc_final: 0.6773 (ttpp) REVERT: B 279 GLU cc_start: 0.8430 (tt0) cc_final: 0.8112 (tt0) REVERT: B 331 MET cc_start: 0.7184 (ttp) cc_final: 0.6940 (ttp) REVERT: B 380 LYS cc_start: 0.7432 (mmtp) cc_final: 0.6980 (mmmt) REVERT: B 399 ARG cc_start: 0.8470 (mtm180) cc_final: 0.7622 (tpt170) REVERT: B 410 SER cc_start: 0.9201 (OUTLIER) cc_final: 0.8746 (m) REVERT: C 126 ARG cc_start: 0.7157 (mtm110) cc_final: 0.6377 (mtm110) REVERT: C 131 ARG cc_start: 0.7716 (tpt-90) cc_final: 0.6158 (tmt-80) REVERT: C 272 LYS cc_start: 0.7298 (tppp) cc_final: 0.6778 (ttpp) REVERT: C 279 GLU cc_start: 0.8437 (tt0) cc_final: 0.8119 (tt0) REVERT: C 331 MET cc_start: 0.7180 (ttp) cc_final: 0.6936 (ttp) REVERT: C 380 LYS cc_start: 0.7435 (mmtp) cc_final: 0.6983 (mmmt) REVERT: C 399 ARG cc_start: 0.8469 (mtm180) cc_final: 0.7624 (tpt170) REVERT: C 410 SER cc_start: 0.9199 (OUTLIER) cc_final: 0.8745 (m) REVERT: D 126 ARG cc_start: 0.7184 (mtm110) cc_final: 0.6387 (mtm110) REVERT: D 131 ARG cc_start: 0.7713 (tpt-90) cc_final: 0.6149 (tmt-80) REVERT: D 272 LYS cc_start: 0.7300 (tppp) cc_final: 0.6781 (ttpp) REVERT: D 331 MET cc_start: 0.7193 (ttp) cc_final: 0.6954 (ttp) REVERT: D 380 LYS cc_start: 0.7428 (mmtp) cc_final: 0.6984 (mmmt) REVERT: D 399 ARG cc_start: 0.8459 (mtm180) cc_final: 0.7636 (tpt170) REVERT: D 410 SER cc_start: 0.9200 (OUTLIER) cc_final: 0.8747 (m) outliers start: 40 outliers final: 16 residues processed: 186 average time/residue: 1.3046 time to fit residues: 263.0314 Evaluate side-chains 178 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 79 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN A 189 GLN A 383 GLN B 171 ASN B 189 GLN B 383 GLN C 171 ASN C 189 GLN C 383 GLN D 171 ASN D 189 GLN D 383 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.157000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.113159 restraints weight = 12117.540| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.60 r_work: 0.3040 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12236 Z= 0.253 Angle : 0.455 5.265 16596 Z= 0.250 Chirality : 0.037 0.131 1988 Planarity : 0.003 0.025 2032 Dihedral : 3.577 13.928 1656 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.75 % Allowed : 18.50 % Favored : 78.75 % 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: 3.10 (0.20), residues: 1504 helix: 2.58 (0.13), residues: 1264 sheet: 0.73 (0.59), residues: 48 loop : -1.49 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 38 HIS 0.002 0.001 HIS A 337 PHE 0.010 0.002 PHE B 392 TYR 0.010 0.001 TYR B 175 ARG 0.003 0.000 ARG D 424 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 1.393 Fit side-chains REVERT: A 51 MET cc_start: 0.8218 (mmt) cc_final: 0.7862 (tpp) REVERT: A 71 MET cc_start: 0.6975 (mmm) cc_final: 0.6359 (mmm) REVERT: A 114 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7148 (mtmt) REVERT: A 126 ARG cc_start: 0.7162 (mtm110) cc_final: 0.6393 (mtm110) REVERT: A 131 ARG cc_start: 0.7672 (tpt-90) cc_final: 0.6066 (tmt-80) REVERT: A 272 LYS cc_start: 0.7270 (tppp) cc_final: 0.6744 (ttpp) REVERT: A 279 GLU cc_start: 0.8502 (tt0) cc_final: 0.8281 (tt0) REVERT: A 283 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8606 (mttt) REVERT: A 331 MET cc_start: 0.7158 (ttp) cc_final: 0.6922 (ttp) REVERT: A 380 LYS cc_start: 0.7373 (mmtp) cc_final: 0.6920 (mmmt) REVERT: A 399 ARG cc_start: 0.8450 (mtm180) cc_final: 0.7573 (tpt170) REVERT: A 410 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8691 (m) REVERT: B 51 MET cc_start: 0.8217 (mmt) cc_final: 0.7940 (tpp) REVERT: B 71 MET cc_start: 0.6972 (mmm) cc_final: 0.6356 (mmm) REVERT: B 114 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7156 (mtmt) REVERT: B 126 ARG cc_start: 0.7165 (mtm110) cc_final: 0.6435 (mtm110) REVERT: B 131 ARG cc_start: 0.7668 (tpt-90) cc_final: 0.6059 (tmt-80) REVERT: B 272 LYS cc_start: 0.7276 (tppp) cc_final: 0.6747 (ttpp) REVERT: B 279 GLU cc_start: 0.8499 (tt0) cc_final: 0.8274 (tt0) REVERT: B 283 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8606 (mttt) REVERT: B 331 MET cc_start: 0.7121 (ttp) cc_final: 0.6880 (ttp) REVERT: B 380 LYS cc_start: 0.7364 (mmtp) cc_final: 0.6908 (mmmt) REVERT: B 399 ARG cc_start: 0.8459 (mtm180) cc_final: 0.7579 (tpt170) REVERT: B 410 SER cc_start: 0.9161 (OUTLIER) cc_final: 0.8701 (m) REVERT: C 51 MET cc_start: 0.8201 (mmt) cc_final: 0.7923 (tpp) REVERT: C 71 MET cc_start: 0.6975 (mmm) cc_final: 0.6321 (mmm) REVERT: C 126 ARG cc_start: 0.7074 (mtm110) cc_final: 0.6329 (mtm110) REVERT: C 131 ARG cc_start: 0.7672 (tpt-90) cc_final: 0.6066 (tmt-80) REVERT: C 272 LYS cc_start: 0.7283 (tppp) cc_final: 0.6754 (ttpp) REVERT: C 279 GLU cc_start: 0.8507 (tt0) cc_final: 0.8287 (tt0) REVERT: C 283 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8607 (mttt) REVERT: C 331 MET cc_start: 0.7111 (ttp) cc_final: 0.6870 (ttp) REVERT: C 380 LYS cc_start: 0.7364 (mmtp) cc_final: 0.6911 (mmmt) REVERT: C 399 ARG cc_start: 0.8458 (mtm180) cc_final: 0.7579 (tpt170) REVERT: C 410 SER cc_start: 0.9148 (OUTLIER) cc_final: 0.8682 (m) REVERT: D 51 MET cc_start: 0.8278 (mmt) cc_final: 0.7971 (tpp) REVERT: D 71 MET cc_start: 0.6990 (mmm) cc_final: 0.6367 (mmm) REVERT: D 126 ARG cc_start: 0.7134 (mtm110) cc_final: 0.6369 (mtm110) REVERT: D 129 ARG cc_start: 0.7867 (ttm-80) cc_final: 0.7415 (ttm170) REVERT: D 131 ARG cc_start: 0.7665 (tpt-90) cc_final: 0.6049 (tmt-80) REVERT: D 272 LYS cc_start: 0.7288 (tppp) cc_final: 0.6755 (ttpp) REVERT: D 331 MET cc_start: 0.7185 (ttp) cc_final: 0.6947 (ttp) REVERT: D 380 LYS cc_start: 0.7360 (mmtp) cc_final: 0.6905 (mmmt) REVERT: D 399 ARG cc_start: 0.8447 (mtm180) cc_final: 0.7592 (tpt170) REVERT: D 410 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8691 (m) outliers start: 36 outliers final: 16 residues processed: 181 average time/residue: 1.3662 time to fit residues: 267.2153 Evaluate side-chains 174 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 23 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 120 optimal weight: 0.0980 chunk 55 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.160217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.117590 restraints weight = 12117.777| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.53 r_work: 0.3057 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12236 Z= 0.140 Angle : 0.391 4.740 16596 Z= 0.218 Chirality : 0.034 0.132 1988 Planarity : 0.003 0.026 2032 Dihedral : 3.386 13.541 1656 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.07 % Allowed : 20.18 % Favored : 78.75 % 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: 3.60 (0.21), residues: 1504 helix: 2.91 (0.13), residues: 1264 sheet: 0.92 (0.52), residues: 48 loop : -1.24 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 154 HIS 0.001 0.000 HIS B 278 PHE 0.009 0.001 PHE C 11 TYR 0.006 0.001 TYR C 96 ARG 0.002 0.000 ARG D 424 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 1.516 Fit side-chains REVERT: A 42 VAL cc_start: 0.7979 (m) cc_final: 0.7732 (t) REVERT: A 51 MET cc_start: 0.8254 (mmt) cc_final: 0.7986 (tpp) REVERT: A 126 ARG cc_start: 0.7196 (mtm110) cc_final: 0.6380 (mtm110) REVERT: A 131 ARG cc_start: 0.7748 (tpt-90) cc_final: 0.6154 (tmt-80) REVERT: A 272 LYS cc_start: 0.7289 (tppp) cc_final: 0.6797 (ttpp) REVERT: A 279 GLU cc_start: 0.8465 (tt0) cc_final: 0.8190 (tt0) REVERT: A 331 MET cc_start: 0.7178 (ttp) cc_final: 0.6937 (ttp) REVERT: A 364 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7109 (mm-30) REVERT: A 380 LYS cc_start: 0.7373 (mmtp) cc_final: 0.6937 (mmmt) REVERT: A 399 ARG cc_start: 0.8377 (mtm180) cc_final: 0.7557 (tpt170) REVERT: A 410 SER cc_start: 0.9207 (OUTLIER) cc_final: 0.8762 (m) REVERT: B 42 VAL cc_start: 0.7975 (m) cc_final: 0.7734 (t) REVERT: B 51 MET cc_start: 0.8236 (mmt) cc_final: 0.8029 (tpp) REVERT: B 126 ARG cc_start: 0.7207 (mtm110) cc_final: 0.6386 (mtm110) REVERT: B 131 ARG cc_start: 0.7748 (tpt-90) cc_final: 0.6155 (tmt-80) REVERT: B 272 LYS cc_start: 0.7285 (tppp) cc_final: 0.6796 (ttpp) REVERT: B 279 GLU cc_start: 0.8449 (tt0) cc_final: 0.8174 (tt0) REVERT: B 331 MET cc_start: 0.7122 (ttp) cc_final: 0.6875 (ttp) REVERT: B 380 LYS cc_start: 0.7374 (mmtp) cc_final: 0.6935 (mmmt) REVERT: B 399 ARG cc_start: 0.8377 (mtm180) cc_final: 0.7563 (tpt170) REVERT: B 410 SER cc_start: 0.9215 (OUTLIER) cc_final: 0.8769 (m) REVERT: C 51 MET cc_start: 0.8225 (mmt) cc_final: 0.8019 (tpp) REVERT: C 126 ARG cc_start: 0.7200 (mtm110) cc_final: 0.6416 (mtm110) REVERT: C 131 ARG cc_start: 0.7742 (tpt-90) cc_final: 0.6156 (tmt-80) REVERT: C 272 LYS cc_start: 0.7302 (tppp) cc_final: 0.6807 (ttpp) REVERT: C 279 GLU cc_start: 0.8462 (tt0) cc_final: 0.8183 (tt0) REVERT: C 331 MET cc_start: 0.7122 (ttp) cc_final: 0.6874 (ttp) REVERT: C 380 LYS cc_start: 0.7368 (mmtp) cc_final: 0.6939 (mmmt) REVERT: C 386 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8143 (tt) REVERT: C 399 ARG cc_start: 0.8380 (mtm180) cc_final: 0.7566 (tpt170) REVERT: C 410 SER cc_start: 0.9212 (OUTLIER) cc_final: 0.8768 (m) REVERT: D 42 VAL cc_start: 0.7973 (m) cc_final: 0.7726 (t) REVERT: D 51 MET cc_start: 0.8269 (mmt) cc_final: 0.7981 (tpp) REVERT: D 126 ARG cc_start: 0.7197 (mtm110) cc_final: 0.6382 (mtm110) REVERT: D 131 ARG cc_start: 0.7747 (tpt-90) cc_final: 0.6150 (tmt-80) REVERT: D 272 LYS cc_start: 0.7295 (tppp) cc_final: 0.6804 (ttpp) REVERT: D 331 MET cc_start: 0.7198 (ttp) cc_final: 0.6958 (ttp) REVERT: D 380 LYS cc_start: 0.7358 (mmtp) cc_final: 0.6934 (mmmt) REVERT: D 386 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8123 (tt) REVERT: D 399 ARG cc_start: 0.8380 (mtm180) cc_final: 0.7580 (tpt170) REVERT: D 410 SER cc_start: 0.9212 (OUTLIER) cc_final: 0.8766 (m) outliers start: 14 outliers final: 4 residues processed: 181 average time/residue: 1.3405 time to fit residues: 263.1961 Evaluate side-chains 170 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 120 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 383 GLN C 383 GLN D 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.155912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.112027 restraints weight = 12061.154| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.60 r_work: 0.2976 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12236 Z= 0.321 Angle : 0.490 5.318 16596 Z= 0.268 Chirality : 0.038 0.131 1988 Planarity : 0.003 0.025 2032 Dihedral : 3.656 14.657 1656 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.06 % Allowed : 19.27 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.20), residues: 1504 helix: 2.51 (0.13), residues: 1264 sheet: 0.65 (0.53), residues: 48 loop : -1.50 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 174 HIS 0.004 0.001 HIS B 337 PHE 0.015 0.002 PHE D 422 TYR 0.011 0.002 TYR A 175 ARG 0.004 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.311 Fit side-chains REVERT: A 71 MET cc_start: 0.6958 (mmm) cc_final: 0.6387 (mmm) REVERT: A 126 ARG cc_start: 0.7322 (mtm110) cc_final: 0.6568 (mtm110) REVERT: A 131 ARG cc_start: 0.7840 (tpt-90) cc_final: 0.6308 (tmt-80) REVERT: A 173 HIS cc_start: 0.6663 (OUTLIER) cc_final: 0.5709 (m-70) REVERT: A 272 LYS cc_start: 0.7407 (tppp) cc_final: 0.6917 (ttpp) REVERT: A 279 GLU cc_start: 0.8580 (tt0) cc_final: 0.8371 (tt0) REVERT: A 283 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8758 (mttt) REVERT: A 331 MET cc_start: 0.7414 (ttp) cc_final: 0.7181 (ttp) REVERT: A 380 LYS cc_start: 0.7512 (mmtp) cc_final: 0.7059 (mmmt) REVERT: A 399 ARG cc_start: 0.8594 (mtm180) cc_final: 0.7734 (tpt170) REVERT: B 71 MET cc_start: 0.6966 (mmm) cc_final: 0.6396 (mmm) REVERT: B 126 ARG cc_start: 0.7341 (mtm110) cc_final: 0.6622 (mtm110) REVERT: B 131 ARG cc_start: 0.7843 (tpt-90) cc_final: 0.6313 (tmt-80) REVERT: B 173 HIS cc_start: 0.6656 (OUTLIER) cc_final: 0.5701 (m-70) REVERT: B 272 LYS cc_start: 0.7403 (tppp) cc_final: 0.6916 (ttpp) REVERT: B 279 GLU cc_start: 0.8571 (tt0) cc_final: 0.8358 (tt0) REVERT: B 331 MET cc_start: 0.7357 (ttp) cc_final: 0.7124 (ttp) REVERT: B 380 LYS cc_start: 0.7508 (mmtp) cc_final: 0.7055 (mmmt) REVERT: B 399 ARG cc_start: 0.8597 (mtm180) cc_final: 0.7740 (tpt170) REVERT: C 71 MET cc_start: 0.6966 (mmm) cc_final: 0.6352 (mmm) REVERT: C 126 ARG cc_start: 0.7363 (mtm110) cc_final: 0.6635 (mtm110) REVERT: C 131 ARG cc_start: 0.7839 (tpt-90) cc_final: 0.6309 (tmt-80) REVERT: C 173 HIS cc_start: 0.6653 (OUTLIER) cc_final: 0.5697 (m-70) REVERT: C 272 LYS cc_start: 0.7411 (tppp) cc_final: 0.6922 (ttpp) REVERT: C 279 GLU cc_start: 0.8585 (tt0) cc_final: 0.8371 (tt0) REVERT: C 331 MET cc_start: 0.7360 (ttp) cc_final: 0.7126 (ttp) REVERT: C 380 LYS cc_start: 0.7503 (mmtp) cc_final: 0.7058 (mmmt) REVERT: C 399 ARG cc_start: 0.8605 (mtm180) cc_final: 0.7741 (tpt170) REVERT: D 51 MET cc_start: 0.8415 (mmt) cc_final: 0.8119 (tpp) REVERT: D 71 MET cc_start: 0.6969 (mmm) cc_final: 0.6396 (mmm) REVERT: D 126 ARG cc_start: 0.7366 (mtm110) cc_final: 0.6603 (mtm110) REVERT: D 131 ARG cc_start: 0.7840 (tpt-90) cc_final: 0.6304 (tmt-80) REVERT: D 173 HIS cc_start: 0.6643 (OUTLIER) cc_final: 0.5685 (m-70) REVERT: D 272 LYS cc_start: 0.7401 (tppp) cc_final: 0.6913 (ttpp) REVERT: D 380 LYS cc_start: 0.7500 (mmtp) cc_final: 0.7054 (mmmt) REVERT: D 399 ARG cc_start: 0.8598 (mtm180) cc_final: 0.7747 (tpt170) outliers start: 27 outliers final: 9 residues processed: 169 average time/residue: 1.3911 time to fit residues: 253.1527 Evaluate side-chains 166 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 404 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 0.0040 chunk 104 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 overall best weight: 1.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 383 GLN C 383 GLN D 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.157236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.113695 restraints weight = 12076.003| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.59 r_work: 0.2999 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12236 Z= 0.225 Angle : 0.443 5.042 16596 Z= 0.245 Chirality : 0.036 0.131 1988 Planarity : 0.003 0.026 2032 Dihedral : 3.580 14.636 1656 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.53 % Allowed : 20.18 % Favored : 78.29 % 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: 3.14 (0.20), residues: 1504 helix: 2.61 (0.13), residues: 1264 sheet: 0.69 (0.49), residues: 48 loop : -1.46 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 154 HIS 0.002 0.001 HIS B 337 PHE 0.010 0.002 PHE D 392 TYR 0.009 0.001 TYR C 175 ARG 0.002 0.000 ARG A 340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.346 Fit side-chains REVERT: A 51 MET cc_start: 0.8434 (mmt) cc_final: 0.8129 (tpp) REVERT: A 71 MET cc_start: 0.6948 (mmm) cc_final: 0.6312 (mmm) REVERT: A 126 ARG cc_start: 0.7325 (mtm110) cc_final: 0.6612 (mtm110) REVERT: A 131 ARG cc_start: 0.7857 (tpt-90) cc_final: 0.6321 (tmt-80) REVERT: A 173 HIS cc_start: 0.6628 (OUTLIER) cc_final: 0.5625 (m-70) REVERT: A 272 LYS cc_start: 0.7398 (tppp) cc_final: 0.6910 (ttpp) REVERT: A 279 GLU cc_start: 0.8565 (tt0) cc_final: 0.8357 (tt0) REVERT: A 283 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8737 (mttt) REVERT: A 331 MET cc_start: 0.7365 (ttp) cc_final: 0.7142 (ttp) REVERT: A 380 LYS cc_start: 0.7504 (mmtp) cc_final: 0.7063 (mmmt) REVERT: A 399 ARG cc_start: 0.8542 (mtm180) cc_final: 0.7721 (tpt170) REVERT: B 71 MET cc_start: 0.6956 (mmm) cc_final: 0.6319 (mmm) REVERT: B 126 ARG cc_start: 0.7326 (mtm110) cc_final: 0.6613 (mtm110) REVERT: B 131 ARG cc_start: 0.7854 (tpt-90) cc_final: 0.6323 (tmt-80) REVERT: B 173 HIS cc_start: 0.6615 (OUTLIER) cc_final: 0.5614 (m-70) REVERT: B 272 LYS cc_start: 0.7391 (tppp) cc_final: 0.6906 (ttpp) REVERT: B 279 GLU cc_start: 0.8552 (tt0) cc_final: 0.8339 (tt0) REVERT: B 331 MET cc_start: 0.7315 (ttp) cc_final: 0.7082 (ttp) REVERT: B 380 LYS cc_start: 0.7501 (mmtp) cc_final: 0.7053 (mmmt) REVERT: B 399 ARG cc_start: 0.8541 (mtm180) cc_final: 0.7726 (tpt170) REVERT: C 71 MET cc_start: 0.6950 (mmm) cc_final: 0.6310 (mmm) REVERT: C 126 ARG cc_start: 0.7370 (mtm110) cc_final: 0.6648 (mtm110) REVERT: C 131 ARG cc_start: 0.7854 (tpt-90) cc_final: 0.6320 (tmt-80) REVERT: C 173 HIS cc_start: 0.6625 (OUTLIER) cc_final: 0.5626 (m-70) REVERT: C 272 LYS cc_start: 0.7404 (tppp) cc_final: 0.6914 (ttpp) REVERT: C 279 GLU cc_start: 0.8565 (tt0) cc_final: 0.8356 (tt0) REVERT: C 283 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8735 (mttt) REVERT: C 331 MET cc_start: 0.7316 (ttp) cc_final: 0.7085 (ttp) REVERT: C 380 LYS cc_start: 0.7494 (mmtp) cc_final: 0.7054 (mmmt) REVERT: C 399 ARG cc_start: 0.8545 (mtm180) cc_final: 0.7726 (tpt170) REVERT: D 51 MET cc_start: 0.8413 (mmt) cc_final: 0.8129 (tpp) REVERT: D 71 MET cc_start: 0.6954 (mmm) cc_final: 0.6319 (mmm) REVERT: D 126 ARG cc_start: 0.7320 (mtm110) cc_final: 0.6608 (mtm110) REVERT: D 131 ARG cc_start: 0.7857 (tpt-90) cc_final: 0.6318 (tmt-80) REVERT: D 173 HIS cc_start: 0.6603 (OUTLIER) cc_final: 0.5593 (m-70) REVERT: D 272 LYS cc_start: 0.7396 (tppp) cc_final: 0.6908 (ttpp) REVERT: D 331 MET cc_start: 0.7384 (ttp) cc_final: 0.7159 (ttp) REVERT: D 380 LYS cc_start: 0.7490 (mmtp) cc_final: 0.7049 (mmmt) REVERT: D 399 ARG cc_start: 0.8548 (mtm180) cc_final: 0.7732 (tpt170) outliers start: 20 outliers final: 9 residues processed: 160 average time/residue: 1.3587 time to fit residues: 234.8337 Evaluate side-chains 163 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 404 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 105 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 383 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.158630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.115211 restraints weight = 11982.841| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.59 r_work: 0.3023 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12236 Z= 0.175 Angle : 0.415 4.938 16596 Z= 0.231 Chirality : 0.035 0.131 1988 Planarity : 0.003 0.026 2032 Dihedral : 3.477 13.549 1656 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.68 % Allowed : 20.03 % Favored : 78.29 % 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: 3.41 (0.20), residues: 1504 helix: 2.80 (0.13), residues: 1264 sheet: 0.80 (0.46), residues: 48 loop : -1.36 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 154 HIS 0.001 0.000 HIS D 349 PHE 0.009 0.001 PHE A 392 TYR 0.007 0.001 TYR B 175 ARG 0.001 0.000 ARG D 424 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9002.62 seconds wall clock time: 160 minutes 39.39 seconds (9639.39 seconds total)