Starting phenix.real_space_refine on Wed Jul 30 00:51:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x82_38133/07_2025/8x82_38133_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x82_38133/07_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_38133/07_2025/8x82_38133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x82_38133/07_2025/8x82_38133.map" model { file = "/net/cci-nas-00/data/ceres_data/8x82_38133/07_2025/8x82_38133_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x82_38133/07_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.27, per 1000 atoms: 0.52 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: 3.22 Conformation dependent library (CDL) restraints added in 1.9 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: 1.55 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: 3.63 Time building geometry restraints manager: 3.76 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: 0.09 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 28.980 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.630 ------------------------------------------------------------------------------- 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= 0.105 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 Details of bonding type rmsd hydrogen bonds : bond 0.10060 ( 1068) hydrogen bonds : angle 4.81661 ( 3204) covalent geometry : bond 0.00207 (12236) covalent geometry : angle 0.40818 (16596) *********************** 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 : 1.361 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: 1.4424 time to fit residues: 295.6384 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 : 1.333 ------------------------------------------------------------------------------- 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 = 0.157700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.112951 restraints weight = 12011.324| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.65 r_work: 0.3036 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1413 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= 0.214 Angle : 0.508 4.891 16596 Z= 0.277 Chirality : 0.039 0.133 1988 Planarity : 0.004 0.025 2032 Dihedral : 3.550 12.488 1656 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.52 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 C 349 PHE 0.013 0.002 PHE A 11 TYR 0.017 0.002 TYR B 175 ARG 0.003 0.001 ARG B 424 Details of bonding type rmsd hydrogen bonds : bond 0.05011 ( 1068) hydrogen bonds : angle 4.23249 ( 3204) covalent geometry : bond 0.00491 (12236) covalent geometry : angle 0.50795 (16596) *********************** 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 : 1.385 Fit side-chains REVERT: A 51 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7866 (mmt) REVERT: A 114 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7299 (mtmt) REVERT: A 126 ARG cc_start: 0.7192 (mtm110) cc_final: 0.6423 (mtm110) REVERT: A 131 ARG cc_start: 0.7668 (mpt-90) cc_final: 0.6151 (tmt-80) REVERT: A 272 LYS cc_start: 0.7324 (tppp) cc_final: 0.6699 (ttpp) REVERT: A 279 GLU cc_start: 0.8512 (tt0) cc_final: 0.8245 (tt0) REVERT: A 399 ARG cc_start: 0.8442 (mtm180) cc_final: 0.7590 (tpt170) REVERT: B 51 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7861 (mmt) REVERT: B 114 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7292 (mtmt) REVERT: B 126 ARG cc_start: 0.7195 (mtm110) cc_final: 0.6423 (mtm110) REVERT: B 131 ARG cc_start: 0.7659 (mpt-90) cc_final: 0.6142 (tmt-80) REVERT: B 272 LYS cc_start: 0.7335 (tppp) cc_final: 0.6696 (ttpp) REVERT: B 279 GLU cc_start: 0.8499 (tt0) cc_final: 0.8231 (tt0) REVERT: B 399 ARG cc_start: 0.8448 (mtm180) cc_final: 0.7594 (tpt170) REVERT: C 51 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7865 (mmt) REVERT: C 114 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7311 (mtmt) REVERT: C 126 ARG cc_start: 0.7189 (mtm110) cc_final: 0.6440 (mtm110) REVERT: C 131 ARG cc_start: 0.7676 (mpt-90) cc_final: 0.6162 (tmt-80) REVERT: C 272 LYS cc_start: 0.7330 (tppp) cc_final: 0.6703 (ttpp) REVERT: C 279 GLU cc_start: 0.8496 (tt0) cc_final: 0.8226 (tt0) REVERT: C 399 ARG cc_start: 0.8439 (mtm180) cc_final: 0.7609 (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: 0.7318 (mtmt) REVERT: D 126 ARG cc_start: 0.7189 (mtm110) cc_final: 0.6419 (mtm110) REVERT: D 131 ARG cc_start: 0.7679 (mpt-90) cc_final: 0.6159 (tmt-80) REVERT: D 272 LYS cc_start: 0.7333 (tppp) cc_final: 0.6706 (ttpp) REVERT: D 279 GLU cc_start: 0.8544 (tt0) cc_final: 0.8335 (tt0) REVERT: D 399 ARG cc_start: 0.8467 (mtm180) cc_final: 0.7642 (tpt170) outliers start: 40 outliers final: 12 residues processed: 172 average time/residue: 1.4148 time to fit residues: 261.6558 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 : 1.260 ------------------------------------------------------------------------------- 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: 0.8980 chunk 16 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 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: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.156919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.111864 restraints weight = 12188.244| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.66 r_work: 0.2976 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12236 Z= 0.189 Angle : 0.477 5.487 16596 Z= 0.262 Chirality : 0.038 0.130 1988 Planarity : 0.003 0.025 2032 Dihedral : 3.643 12.828 1656 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: 2.90 (0.21), residues: 1504 helix: 2.41 (0.13), residues: 1264 sheet: 1.15 (0.73), residues: 48 loop : -1.40 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 130 HIS 0.002 0.001 HIS D 337 PHE 0.013 0.002 PHE D 422 TYR 0.012 0.001 TYR B 175 ARG 0.003 0.000 ARG A 424 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 1068) hydrogen bonds : angle 4.17299 ( 3204) covalent geometry : bond 0.00430 (12236) covalent geometry : angle 0.47729 (16596) *********************** 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 173 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 1.333 Fit side-chains REVERT: A 25 VAL cc_start: 0.8085 (p) cc_final: 0.7883 (m) REVERT: A 126 ARG cc_start: 0.7244 (mtm110) cc_final: 0.6502 (mtm110) REVERT: A 131 ARG cc_start: 0.7795 (mpt-90) cc_final: 0.6283 (tmt-80) REVERT: A 272 LYS cc_start: 0.7371 (tppp) cc_final: 0.6841 (ttpp) REVERT: A 279 GLU cc_start: 0.8540 (tt0) cc_final: 0.8266 (tt0) REVERT: A 313 PHE cc_start: 0.7009 (OUTLIER) cc_final: 0.6575 (m-10) REVERT: A 399 ARG cc_start: 0.8542 (mtm180) cc_final: 0.7659 (tpt170) REVERT: A 410 SER cc_start: 0.9251 (OUTLIER) cc_final: 0.8818 (m) REVERT: B 25 VAL cc_start: 0.8108 (p) cc_final: 0.7900 (m) REVERT: B 126 ARG cc_start: 0.7243 (mtm110) cc_final: 0.6498 (mtm110) REVERT: B 131 ARG cc_start: 0.7795 (mpt-90) cc_final: 0.6286 (tmt-80) REVERT: B 279 GLU cc_start: 0.8532 (tt0) cc_final: 0.8258 (tt0) REVERT: B 313 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.6585 (m-10) REVERT: B 399 ARG cc_start: 0.8549 (mtm180) cc_final: 0.7673 (tpt170) REVERT: B 410 SER cc_start: 0.9254 (OUTLIER) cc_final: 0.8821 (m) REVERT: C 25 VAL cc_start: 0.8113 (p) cc_final: 0.7907 (m) REVERT: C 126 ARG cc_start: 0.7244 (mtm110) cc_final: 0.6499 (mtm110) REVERT: C 131 ARG cc_start: 0.7797 (mpt-90) cc_final: 0.6287 (tmt-80) REVERT: C 279 GLU cc_start: 0.8537 (tt0) cc_final: 0.8263 (tt0) REVERT: C 313 PHE cc_start: 0.7014 (OUTLIER) cc_final: 0.6583 (m-10) REVERT: C 399 ARG cc_start: 0.8541 (mtm180) cc_final: 0.7668 (tpt170) REVERT: C 410 SER cc_start: 0.9258 (OUTLIER) cc_final: 0.8826 (m) REVERT: D 25 VAL cc_start: 0.8095 (p) cc_final: 0.7893 (m) REVERT: D 126 ARG cc_start: 0.7235 (mtm110) cc_final: 0.6491 (mtm110) REVERT: D 131 ARG cc_start: 0.7795 (mpt-90) cc_final: 0.6284 (tmt-80) REVERT: D 313 PHE cc_start: 0.7013 (OUTLIER) cc_final: 0.6579 (m-10) REVERT: D 399 ARG cc_start: 0.8549 (mtm180) cc_final: 0.7666 (tpt170) REVERT: D 410 SER cc_start: 0.9256 (OUTLIER) cc_final: 0.8823 (m) outliers start: 36 outliers final: 12 residues processed: 161 average time/residue: 1.2430 time to fit residues: 217.6602 Evaluate side-chains 153 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 1.368 ------------------------------------------------------------------------------- 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: 0.7980 chunk 85 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.157818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.113982 restraints weight = 12102.089| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.61 r_work: 0.3050 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12236 Z= 0.149 Angle : 0.432 5.348 16596 Z= 0.239 Chirality : 0.036 0.131 1988 Planarity : 0.003 0.026 2032 Dihedral : 3.550 12.718 1656 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.36 % Allowed : 16.21 % Favored : 80.43 % 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: 3.13 (0.21), residues: 1504 helix: 2.58 (0.13), residues: 1264 sheet: 1.04 (0.68), residues: 48 loop : -1.38 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 154 HIS 0.002 0.001 HIS D 337 PHE 0.011 0.002 PHE C 11 TYR 0.009 0.001 TYR A 175 ARG 0.002 0.000 ARG C 340 Details of bonding type rmsd hydrogen bonds : bond 0.04430 ( 1068) hydrogen bonds : angle 4.03984 ( 3204) covalent geometry : bond 0.00325 (12236) covalent geometry : angle 0.43192 (16596) *********************** 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 206 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 1.317 Fit side-chains REVERT: A 126 ARG cc_start: 0.7052 (mtm110) cc_final: 0.6300 (mtm110) REVERT: A 129 ARG cc_start: 0.7895 (ttm-80) cc_final: 0.7632 (ttm170) REVERT: A 131 ARG cc_start: 0.7637 (mpt-90) cc_final: 0.6087 (tmt-80) REVERT: A 173 HIS cc_start: 0.6478 (OUTLIER) cc_final: 0.5559 (m-70) REVERT: A 272 LYS cc_start: 0.7317 (tppp) cc_final: 0.6772 (ttpp) REVERT: A 279 GLU cc_start: 0.8440 (tt0) cc_final: 0.8096 (tt0) REVERT: A 364 GLU cc_start: 0.7255 (mt-10) cc_final: 0.7020 (mm-30) REVERT: A 380 LYS cc_start: 0.7342 (mmtp) cc_final: 0.6902 (mmmt) REVERT: A 399 ARG cc_start: 0.8420 (mtm180) cc_final: 0.7544 (tpt170) REVERT: A 410 SER cc_start: 0.9138 (OUTLIER) cc_final: 0.8692 (m) REVERT: B 126 ARG cc_start: 0.7065 (mtm110) cc_final: 0.6312 (mtm110) REVERT: B 129 ARG cc_start: 0.7901 (ttm-80) cc_final: 0.7638 (ttm170) REVERT: B 131 ARG cc_start: 0.7641 (mpt-90) cc_final: 0.6093 (tmt-80) REVERT: B 173 HIS cc_start: 0.6562 (OUTLIER) cc_final: 0.5680 (m-70) REVERT: B 272 LYS cc_start: 0.7200 (tppp) cc_final: 0.6651 (ttpp) REVERT: B 279 GLU cc_start: 0.8416 (tt0) cc_final: 0.8073 (tt0) REVERT: B 364 GLU cc_start: 0.7305 (mt-10) cc_final: 0.7054 (mm-30) REVERT: B 380 LYS cc_start: 0.7351 (mmtp) cc_final: 0.6910 (mmmt) REVERT: B 399 ARG cc_start: 0.8430 (mtm180) cc_final: 0.7554 (tpt170) REVERT: B 410 SER cc_start: 0.9142 (OUTLIER) cc_final: 0.8698 (m) REVERT: C 126 ARG cc_start: 0.7069 (mtm110) cc_final: 0.6320 (mtm110) REVERT: C 129 ARG cc_start: 0.7897 (ttm-80) cc_final: 0.7630 (ttm170) REVERT: C 131 ARG cc_start: 0.7648 (mpt-90) cc_final: 0.6095 (tmt-80) REVERT: C 173 HIS cc_start: 0.6574 (OUTLIER) cc_final: 0.5694 (m-70) REVERT: C 272 LYS cc_start: 0.7292 (tppp) cc_final: 0.6750 (ttpp) REVERT: C 279 GLU cc_start: 0.8441 (tt0) cc_final: 0.8099 (tt0) REVERT: C 364 GLU cc_start: 0.7302 (mt-10) cc_final: 0.7052 (mm-30) REVERT: C 380 LYS cc_start: 0.7353 (mmtp) cc_final: 0.6920 (mmmt) REVERT: C 399 ARG cc_start: 0.8412 (mtm180) cc_final: 0.7541 (tpt170) REVERT: C 410 SER cc_start: 0.9139 (OUTLIER) cc_final: 0.8693 (m) REVERT: D 126 ARG cc_start: 0.7047 (mtm110) cc_final: 0.6297 (mtm110) REVERT: D 129 ARG cc_start: 0.7890 (ttm-80) cc_final: 0.7624 (ttm170) REVERT: D 131 ARG cc_start: 0.7642 (mpt-90) cc_final: 0.6084 (tmt-80) REVERT: D 173 HIS cc_start: 0.6562 (OUTLIER) cc_final: 0.5681 (m-70) REVERT: D 272 LYS cc_start: 0.7293 (tppp) cc_final: 0.6737 (ttpp) REVERT: D 331 MET cc_start: 0.7091 (ttp) cc_final: 0.6838 (ttp) REVERT: D 364 GLU cc_start: 0.7303 (mt-10) cc_final: 0.7055 (mm-30) REVERT: D 380 LYS cc_start: 0.7345 (mmtp) cc_final: 0.6911 (mmmt) REVERT: D 399 ARG cc_start: 0.8434 (mtm180) cc_final: 0.7564 (tpt170) REVERT: D 410 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8699 (m) outliers start: 44 outliers final: 16 residues processed: 186 average time/residue: 1.3491 time to fit residues: 271.0314 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 : 1.651 ------------------------------------------------------------------------------- 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 173 HIS 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 173 HIS 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 173 HIS 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 173 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 92 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.157646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.114913 restraints weight = 12094.680| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.52 r_work: 0.3021 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12236 Z= 0.149 Angle : 0.436 5.346 16596 Z= 0.240 Chirality : 0.035 0.130 1988 Planarity : 0.003 0.026 2032 Dihedral : 3.527 12.606 1656 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.13 % Allowed : 16.82 % Favored : 80.05 % 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: 3.22 (0.21), residues: 1504 helix: 2.64 (0.13), residues: 1264 sheet: 1.25 (0.66), residues: 48 loop : -1.41 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 154 HIS 0.001 0.001 HIS A 337 PHE 0.010 0.002 PHE A 11 TYR 0.010 0.001 TYR B 175 ARG 0.003 0.000 ARG B 424 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 1068) hydrogen bonds : angle 4.00226 ( 3204) covalent geometry : bond 0.00329 (12236) covalent geometry : angle 0.43627 (16596) *********************** 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 201 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 1.208 Fit side-chains REVERT: A 51 MET cc_start: 0.8409 (tpp) cc_final: 0.8197 (mmt) REVERT: A 114 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7205 (mtmt) REVERT: A 126 ARG cc_start: 0.7109 (mtm110) cc_final: 0.6379 (mtm110) REVERT: A 131 ARG cc_start: 0.7690 (mpt-90) cc_final: 0.6142 (ttt180) REVERT: A 173 HIS cc_start: 0.6585 (OUTLIER) cc_final: 0.5626 (m-70) REVERT: A 272 LYS cc_start: 0.7272 (tppp) cc_final: 0.6724 (ttpp) REVERT: A 279 GLU cc_start: 0.8440 (tt0) cc_final: 0.8099 (tt0) REVERT: A 331 MET cc_start: 0.7092 (ttp) cc_final: 0.6848 (ttp) REVERT: A 364 GLU cc_start: 0.7344 (mt-10) cc_final: 0.7091 (mm-30) REVERT: A 380 LYS cc_start: 0.7382 (mmtp) cc_final: 0.6940 (mmmt) REVERT: A 399 ARG cc_start: 0.8442 (mtm180) cc_final: 0.7554 (tpt170) REVERT: A 410 SER cc_start: 0.9167 (OUTLIER) cc_final: 0.8721 (m) REVERT: B 51 MET cc_start: 0.8422 (tpp) cc_final: 0.8213 (mmt) REVERT: B 71 MET cc_start: 0.7008 (mmm) cc_final: 0.6384 (mmm) REVERT: B 126 ARG cc_start: 0.7110 (mtm110) cc_final: 0.6381 (mtm110) REVERT: B 131 ARG cc_start: 0.7695 (mpt-90) cc_final: 0.6149 (ttt180) REVERT: B 173 HIS cc_start: 0.6571 (OUTLIER) cc_final: 0.5651 (m-70) REVERT: B 272 LYS cc_start: 0.7237 (tppp) cc_final: 0.6700 (ttpp) REVERT: B 279 GLU cc_start: 0.8425 (tt0) cc_final: 0.8083 (tt0) REVERT: B 331 MET cc_start: 0.7107 (ttp) cc_final: 0.6862 (ttp) REVERT: B 364 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7072 (mm-30) REVERT: B 380 LYS cc_start: 0.7395 (mmtp) cc_final: 0.6951 (mmmt) REVERT: B 399 ARG cc_start: 0.8442 (mtm180) cc_final: 0.7569 (tpt170) REVERT: B 410 SER cc_start: 0.9170 (OUTLIER) cc_final: 0.8724 (m) REVERT: C 51 MET cc_start: 0.8422 (tpp) cc_final: 0.8213 (mmt) REVERT: C 126 ARG cc_start: 0.7092 (mtm110) cc_final: 0.6369 (mtm110) REVERT: C 131 ARG cc_start: 0.7695 (mpt-90) cc_final: 0.6152 (ttt180) REVERT: C 173 HIS cc_start: 0.6572 (OUTLIER) cc_final: 0.5653 (m-70) REVERT: C 272 LYS cc_start: 0.7242 (tppp) cc_final: 0.6706 (ttpp) REVERT: C 279 GLU cc_start: 0.8434 (tt0) cc_final: 0.8090 (tt0) REVERT: C 331 MET cc_start: 0.7100 (ttp) cc_final: 0.6855 (ttp) REVERT: C 364 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7069 (mm-30) REVERT: C 380 LYS cc_start: 0.7387 (mmtp) cc_final: 0.6946 (mmmt) REVERT: C 399 ARG cc_start: 0.8435 (mtm180) cc_final: 0.7570 (tpt170) REVERT: C 410 SER cc_start: 0.9167 (OUTLIER) cc_final: 0.8720 (m) REVERT: D 51 MET cc_start: 0.8406 (tpp) cc_final: 0.8194 (mmt) REVERT: D 126 ARG cc_start: 0.7087 (mtm110) cc_final: 0.6364 (mtm110) REVERT: D 131 ARG cc_start: 0.7692 (mpt-90) cc_final: 0.6145 (ttt180) REVERT: D 173 HIS cc_start: 0.6563 (OUTLIER) cc_final: 0.5642 (m-70) REVERT: D 272 LYS cc_start: 0.7250 (tppp) cc_final: 0.6718 (ttpp) REVERT: D 331 MET cc_start: 0.7102 (ttp) cc_final: 0.6857 (ttp) REVERT: D 364 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7061 (mm-30) REVERT: D 380 LYS cc_start: 0.7381 (mmtp) cc_final: 0.6942 (mmmt) REVERT: D 399 ARG cc_start: 0.8446 (mtm180) cc_final: 0.7578 (tpt170) REVERT: D 410 SER cc_start: 0.9171 (OUTLIER) cc_final: 0.8724 (m) outliers start: 41 outliers final: 16 residues processed: 193 average time/residue: 1.4585 time to fit residues: 305.5435 Evaluate side-chains 182 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 1.416 ------------------------------------------------------------------------------- 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 173 HIS 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 173 HIS 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 173 HIS 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 173 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 66 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 B 189 GLN B 383 GLN C 189 GLN D 189 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.159119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.116452 restraints weight = 12229.706| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.53 r_work: 0.3083 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12236 Z= 0.125 Angle : 0.409 5.161 16596 Z= 0.226 Chirality : 0.035 0.132 1988 Planarity : 0.003 0.026 2032 Dihedral : 3.448 13.089 1656 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.83 % Allowed : 19.04 % 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: 3.44 (0.21), residues: 1504 helix: 2.80 (0.13), residues: 1264 sheet: 1.04 (0.59), residues: 48 loop : -1.29 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.001 0.000 HIS D 278 PHE 0.009 0.001 PHE C 11 TYR 0.007 0.001 TYR A 175 ARG 0.002 0.000 ARG B 367 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 1068) hydrogen bonds : angle 3.90168 ( 3204) covalent geometry : bond 0.00261 (12236) covalent geometry : angle 0.40873 (16596) *********************** 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 184 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 1.421 Fit side-chains REVERT: A 51 MET cc_start: 0.8437 (tpp) cc_final: 0.8202 (mmt) REVERT: A 126 ARG cc_start: 0.7085 (mtm110) cc_final: 0.6361 (mtm110) REVERT: A 131 ARG cc_start: 0.7640 (tpt-90) cc_final: 0.6089 (ttt180) REVERT: A 173 HIS cc_start: 0.6564 (OUTLIER) cc_final: 0.5613 (m-70) REVERT: A 272 LYS cc_start: 0.7341 (tppp) cc_final: 0.6830 (ttpp) REVERT: A 279 GLU cc_start: 0.8402 (tt0) cc_final: 0.8049 (tt0) REVERT: A 283 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8564 (mttt) REVERT: A 331 MET cc_start: 0.7075 (ttp) cc_final: 0.6830 (ttp) REVERT: A 364 GLU cc_start: 0.7308 (mt-10) cc_final: 0.7060 (mm-30) REVERT: A 380 LYS cc_start: 0.7371 (mmtp) cc_final: 0.6921 (mmmt) REVERT: A 399 ARG cc_start: 0.8384 (mtm180) cc_final: 0.7541 (tpt170) REVERT: B 51 MET cc_start: 0.8439 (tpp) cc_final: 0.8202 (mmt) REVERT: B 126 ARG cc_start: 0.7095 (mtm110) cc_final: 0.6370 (mtm110) REVERT: B 131 ARG cc_start: 0.7650 (tpt-90) cc_final: 0.6100 (ttt180) REVERT: B 173 HIS cc_start: 0.6568 (OUTLIER) cc_final: 0.5624 (m-70) REVERT: B 272 LYS cc_start: 0.7263 (tppp) cc_final: 0.6738 (ttpp) REVERT: B 279 GLU cc_start: 0.8384 (tt0) cc_final: 0.8032 (tt0) REVERT: B 283 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8559 (mttt) REVERT: B 331 MET cc_start: 0.7087 (ttp) cc_final: 0.6840 (ttp) REVERT: B 364 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6988 (mm-30) REVERT: B 380 LYS cc_start: 0.7372 (mmtp) cc_final: 0.6916 (mmmt) REVERT: B 399 ARG cc_start: 0.8386 (mtm180) cc_final: 0.7543 (tpt170) REVERT: C 51 MET cc_start: 0.8445 (tpp) cc_final: 0.8209 (mmt) REVERT: C 126 ARG cc_start: 0.7080 (mtm110) cc_final: 0.6360 (mtm110) REVERT: C 131 ARG cc_start: 0.7650 (tpt-90) cc_final: 0.6104 (ttt180) REVERT: C 173 HIS cc_start: 0.6573 (OUTLIER) cc_final: 0.5630 (m-70) REVERT: C 272 LYS cc_start: 0.7337 (tppp) cc_final: 0.6844 (ttpp) REVERT: C 279 GLU cc_start: 0.8396 (tt0) cc_final: 0.8042 (tt0) REVERT: C 283 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8568 (mttt) REVERT: C 331 MET cc_start: 0.7079 (ttp) cc_final: 0.6831 (ttp) REVERT: C 364 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6986 (mm-30) REVERT: C 380 LYS cc_start: 0.7365 (mmtp) cc_final: 0.6911 (mmmt) REVERT: C 399 ARG cc_start: 0.8374 (mtm180) cc_final: 0.7539 (tpt170) REVERT: D 51 MET cc_start: 0.8427 (tpp) cc_final: 0.8191 (mmt) REVERT: D 126 ARG cc_start: 0.7069 (mtm110) cc_final: 0.6340 (mtm110) REVERT: D 131 ARG cc_start: 0.7641 (tpt-90) cc_final: 0.6084 (ttt180) REVERT: D 173 HIS cc_start: 0.6565 (OUTLIER) cc_final: 0.5623 (m-70) REVERT: D 272 LYS cc_start: 0.7330 (tppp) cc_final: 0.6830 (ttpp) REVERT: D 331 MET cc_start: 0.7102 (ttp) cc_final: 0.6856 (ttp) REVERT: D 364 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6989 (mm-30) REVERT: D 380 LYS cc_start: 0.7364 (mmtp) cc_final: 0.6917 (mmmt) REVERT: D 399 ARG cc_start: 0.8381 (mtm180) cc_final: 0.7550 (tpt170) outliers start: 24 outliers final: 7 residues processed: 178 average time/residue: 1.6513 time to fit residues: 318.1238 Evaluate side-chains 170 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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 345 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 173 HIS 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 C residue 173 HIS Chi-restraints excluded: chain C residue 283 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 79 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN A 383 GLN B 171 ASN B 383 GLN C 383 GLN D 171 ASN D 383 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.158847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.115196 restraints weight = 12150.559| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.60 r_work: 0.3019 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12236 Z= 0.129 Angle : 0.412 5.112 16596 Z= 0.228 Chirality : 0.035 0.131 1988 Planarity : 0.003 0.026 2032 Dihedral : 3.433 12.692 1656 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.06 % Allowed : 19.88 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.45 (0.21), residues: 1504 helix: 2.81 (0.13), residues: 1264 sheet: 0.87 (0.56), residues: 48 loop : -1.29 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 154 HIS 0.001 0.000 HIS A 278 PHE 0.010 0.001 PHE B 422 TYR 0.007 0.001 TYR D 175 ARG 0.002 0.000 ARG A 424 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 1068) hydrogen bonds : angle 3.87779 ( 3204) covalent geometry : bond 0.00274 (12236) covalent geometry : angle 0.41246 (16596) *********************** 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 182 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.212 Fit side-chains REVERT: A 51 MET cc_start: 0.8510 (tpp) cc_final: 0.8296 (mmt) REVERT: A 126 ARG cc_start: 0.7253 (mtm110) cc_final: 0.6488 (mtm110) REVERT: A 131 ARG cc_start: 0.7814 (tpt-90) cc_final: 0.6302 (ttt180) REVERT: A 173 HIS cc_start: 0.6574 (OUTLIER) cc_final: 0.5634 (m-70) REVERT: A 272 LYS cc_start: 0.7429 (tppp) cc_final: 0.6972 (ttpp) REVERT: A 279 GLU cc_start: 0.8480 (tt0) cc_final: 0.8151 (tt0) REVERT: A 283 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8678 (mttt) REVERT: A 331 MET cc_start: 0.7281 (ttp) cc_final: 0.7035 (ttp) REVERT: A 364 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7248 (mm-30) REVERT: A 380 LYS cc_start: 0.7488 (mmtp) cc_final: 0.7057 (mmmt) REVERT: A 399 ARG cc_start: 0.8483 (mtm180) cc_final: 0.7654 (tpt170) REVERT: A 410 SER cc_start: 0.9265 (OUTLIER) cc_final: 0.8824 (m) REVERT: B 51 MET cc_start: 0.8512 (tpp) cc_final: 0.8300 (mmt) REVERT: B 126 ARG cc_start: 0.7268 (mtm110) cc_final: 0.6465 (mtm110) REVERT: B 131 ARG cc_start: 0.7812 (tpt-90) cc_final: 0.6305 (ttt180) REVERT: B 173 HIS cc_start: 0.6567 (OUTLIER) cc_final: 0.5646 (m-70) REVERT: B 272 LYS cc_start: 0.7370 (tppp) cc_final: 0.6881 (ttpp) REVERT: B 279 GLU cc_start: 0.8476 (tt0) cc_final: 0.8148 (tt0) REVERT: B 283 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8684 (mttt) REVERT: B 331 MET cc_start: 0.7295 (ttp) cc_final: 0.7047 (ttp) REVERT: B 364 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7140 (mm-30) REVERT: B 380 LYS cc_start: 0.7489 (mmtp) cc_final: 0.7058 (mmmt) REVERT: B 399 ARG cc_start: 0.8487 (mtm180) cc_final: 0.7672 (tpt170) REVERT: B 410 SER cc_start: 0.9269 (OUTLIER) cc_final: 0.8828 (m) REVERT: C 51 MET cc_start: 0.8511 (tpp) cc_final: 0.8298 (mmt) REVERT: C 126 ARG cc_start: 0.7260 (mtm110) cc_final: 0.6461 (mtm110) REVERT: C 131 ARG cc_start: 0.7810 (tpt-90) cc_final: 0.6304 (ttt180) REVERT: C 173 HIS cc_start: 0.6577 (OUTLIER) cc_final: 0.5657 (m-70) REVERT: C 272 LYS cc_start: 0.7444 (tppp) cc_final: 0.6980 (ttpp) REVERT: C 279 GLU cc_start: 0.8479 (tt0) cc_final: 0.8150 (tt0) REVERT: C 283 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8682 (mttt) REVERT: C 331 MET cc_start: 0.7289 (ttp) cc_final: 0.7042 (ttp) REVERT: C 364 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7143 (mm-30) REVERT: C 380 LYS cc_start: 0.7487 (mmtp) cc_final: 0.7058 (mmmt) REVERT: C 399 ARG cc_start: 0.8484 (mtm180) cc_final: 0.7674 (tpt170) REVERT: C 410 SER cc_start: 0.9272 (OUTLIER) cc_final: 0.8827 (m) REVERT: D 51 MET cc_start: 0.8507 (tpp) cc_final: 0.8293 (mmt) REVERT: D 126 ARG cc_start: 0.7247 (mtm110) cc_final: 0.6482 (mtm110) REVERT: D 131 ARG cc_start: 0.7811 (tpt-90) cc_final: 0.6300 (ttt180) REVERT: D 173 HIS cc_start: 0.6569 (OUTLIER) cc_final: 0.5650 (m-70) REVERT: D 272 LYS cc_start: 0.7427 (tppp) cc_final: 0.6963 (ttpp) REVERT: D 331 MET cc_start: 0.7294 (ttp) cc_final: 0.7046 (ttp) REVERT: D 364 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7134 (mm-30) REVERT: D 380 LYS cc_start: 0.7481 (mmtp) cc_final: 0.7050 (mmmt) REVERT: D 399 ARG cc_start: 0.8488 (mtm180) cc_final: 0.7690 (tpt170) REVERT: D 410 SER cc_start: 0.9271 (OUTLIER) cc_final: 0.8826 (m) outliers start: 27 outliers final: 8 residues processed: 174 average time/residue: 1.3451 time to fit residues: 252.7949 Evaluate side-chains 174 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 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 345 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 173 HIS 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 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 C residue 410 SER Chi-restraints excluded: chain D residue 173 HIS 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: 0.7980 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 383 GLN C 171 ASN C 383 GLN D 383 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.159371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.116700 restraints weight = 12161.592| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.53 r_work: 0.3087 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12236 Z= 0.123 Angle : 0.407 5.099 16596 Z= 0.224 Chirality : 0.035 0.133 1988 Planarity : 0.003 0.026 2032 Dihedral : 3.410 12.585 1656 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.29 % Allowed : 19.04 % 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: 3.51 (0.21), residues: 1504 helix: 2.86 (0.13), residues: 1264 sheet: 0.78 (0.54), residues: 48 loop : -1.27 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 154 HIS 0.001 0.000 HIS D 278 PHE 0.009 0.001 PHE C 315 TYR 0.007 0.001 TYR D 175 ARG 0.001 0.000 ARG C 367 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 1068) hydrogen bonds : angle 3.84177 ( 3204) covalent geometry : bond 0.00259 (12236) covalent geometry : angle 0.40705 (16596) *********************** 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 186 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 1.334 Fit side-chains REVERT: A 51 MET cc_start: 0.8458 (tpp) cc_final: 0.8223 (mmt) REVERT: A 126 ARG cc_start: 0.7143 (mtm110) cc_final: 0.6329 (mtm110) REVERT: A 131 ARG cc_start: 0.7650 (tpt-90) cc_final: 0.6092 (ttt180) REVERT: A 173 HIS cc_start: 0.6471 (OUTLIER) cc_final: 0.5534 (m-70) REVERT: A 272 LYS cc_start: 0.7312 (tppp) cc_final: 0.6851 (ttpp) REVERT: A 279 GLU cc_start: 0.8398 (tt0) cc_final: 0.8040 (tt0) REVERT: A 283 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8563 (mttt) REVERT: A 331 MET cc_start: 0.7083 (ttp) cc_final: 0.6837 (ttp) REVERT: A 364 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7060 (mm-30) REVERT: A 380 LYS cc_start: 0.7381 (mmtp) cc_final: 0.6929 (mmmt) REVERT: A 399 ARG cc_start: 0.8361 (mtm180) cc_final: 0.7538 (tpt170) REVERT: A 410 SER cc_start: 0.9177 (OUTLIER) cc_final: 0.8707 (m) REVERT: B 51 MET cc_start: 0.8443 (tpp) cc_final: 0.8207 (mmt) REVERT: B 126 ARG cc_start: 0.7149 (mtm110) cc_final: 0.6337 (mtm110) REVERT: B 131 ARG cc_start: 0.7661 (tpt-90) cc_final: 0.6104 (ttt180) REVERT: B 173 HIS cc_start: 0.6459 (OUTLIER) cc_final: 0.5499 (m-70) REVERT: B 272 LYS cc_start: 0.7272 (tppp) cc_final: 0.6772 (ttpp) REVERT: B 279 GLU cc_start: 0.8385 (tt0) cc_final: 0.8026 (tt0) REVERT: B 283 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8559 (mttt) REVERT: B 331 MET cc_start: 0.7084 (ttp) cc_final: 0.6836 (ttp) REVERT: B 364 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7004 (mm-30) REVERT: B 380 LYS cc_start: 0.7379 (mmtp) cc_final: 0.6926 (mmmt) REVERT: B 399 ARG cc_start: 0.8366 (mtm180) cc_final: 0.7544 (tpt170) REVERT: B 410 SER cc_start: 0.9180 (OUTLIER) cc_final: 0.8709 (m) REVERT: C 51 MET cc_start: 0.8465 (tpp) cc_final: 0.8236 (mmt) REVERT: C 126 ARG cc_start: 0.7150 (mtm110) cc_final: 0.6341 (mtm110) REVERT: C 131 ARG cc_start: 0.7663 (tpt-90) cc_final: 0.6112 (ttt180) REVERT: C 173 HIS cc_start: 0.6474 (OUTLIER) cc_final: 0.5516 (m-70) REVERT: C 272 LYS cc_start: 0.7333 (tppp) cc_final: 0.6871 (ttpp) REVERT: C 279 GLU cc_start: 0.8389 (tt0) cc_final: 0.8028 (tt0) REVERT: C 283 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8558 (mttt) REVERT: C 331 MET cc_start: 0.7090 (ttp) cc_final: 0.6843 (ttp) REVERT: C 364 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6997 (mm-30) REVERT: C 380 LYS cc_start: 0.7376 (mmtp) cc_final: 0.6924 (mmmt) REVERT: C 399 ARG cc_start: 0.8350 (mtm180) cc_final: 0.7545 (tpt170) REVERT: C 410 SER cc_start: 0.9177 (OUTLIER) cc_final: 0.8704 (m) REVERT: D 51 MET cc_start: 0.8444 (tpp) cc_final: 0.8209 (mmt) REVERT: D 126 ARG cc_start: 0.7122 (mtm110) cc_final: 0.6303 (mtm110) REVERT: D 131 ARG cc_start: 0.7654 (tpt-90) cc_final: 0.6089 (ttt180) REVERT: D 173 HIS cc_start: 0.6470 (OUTLIER) cc_final: 0.5513 (m-70) REVERT: D 272 LYS cc_start: 0.7325 (tppp) cc_final: 0.6855 (ttpp) REVERT: D 283 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8575 (mttt) REVERT: D 331 MET cc_start: 0.7101 (ttp) cc_final: 0.6856 (ttp) REVERT: D 364 GLU cc_start: 0.7257 (mt-10) cc_final: 0.7001 (mm-30) REVERT: D 380 LYS cc_start: 0.7370 (mmtp) cc_final: 0.6924 (mmmt) REVERT: D 399 ARG cc_start: 0.8363 (mtm180) cc_final: 0.7566 (tpt170) REVERT: D 410 SER cc_start: 0.9170 (OUTLIER) cc_final: 0.8698 (m) outliers start: 30 outliers final: 8 residues processed: 178 average time/residue: 1.3423 time to fit residues: 258.2009 Evaluate side-chains 175 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 345 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 173 HIS 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 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 C residue 410 SER Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 283 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 120 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.159332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.116757 restraints weight = 12080.765| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.53 r_work: 0.3047 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12236 Z= 0.124 Angle : 0.409 5.073 16596 Z= 0.225 Chirality : 0.035 0.132 1988 Planarity : 0.003 0.026 2032 Dihedral : 3.406 12.516 1656 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.99 % Allowed : 19.65 % Favored : 78.36 % 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: 3.53 (0.21), residues: 1504 helix: 2.87 (0.13), residues: 1264 sheet: 0.69 (0.52), residues: 48 loop : -1.25 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 154 HIS 0.001 0.000 HIS A 349 PHE 0.009 0.001 PHE C 422 TYR 0.006 0.001 TYR B 175 ARG 0.001 0.000 ARG C 367 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 1068) hydrogen bonds : angle 3.83138 ( 3204) covalent geometry : bond 0.00262 (12236) covalent geometry : angle 0.40859 (16596) *********************** 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 184 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 2.655 Fit side-chains REVERT: A 51 MET cc_start: 0.8456 (tpp) cc_final: 0.8226 (mmt) REVERT: A 126 ARG cc_start: 0.7180 (mtm110) cc_final: 0.6371 (mtm110) REVERT: A 131 ARG cc_start: 0.7730 (tpt-90) cc_final: 0.6130 (tmt-80) REVERT: A 173 HIS cc_start: 0.6523 (OUTLIER) cc_final: 0.5539 (m-70) REVERT: A 272 LYS cc_start: 0.7343 (tppp) cc_final: 0.6859 (ttpp) REVERT: A 279 GLU cc_start: 0.8426 (tt0) cc_final: 0.8071 (tt0) REVERT: A 283 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8601 (mttt) REVERT: A 331 MET cc_start: 0.7118 (ttp) cc_final: 0.6871 (ttp) REVERT: A 364 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7094 (mm-30) REVERT: A 380 LYS cc_start: 0.7385 (mmtp) cc_final: 0.6947 (mmmt) REVERT: A 399 ARG cc_start: 0.8393 (mtm180) cc_final: 0.7564 (tpt170) REVERT: A 410 SER cc_start: 0.9210 (OUTLIER) cc_final: 0.8753 (m) REVERT: B 51 MET cc_start: 0.8454 (tpp) cc_final: 0.8225 (mmt) REVERT: B 126 ARG cc_start: 0.7199 (mtm110) cc_final: 0.6389 (mtm110) REVERT: B 131 ARG cc_start: 0.7731 (tpt-90) cc_final: 0.6137 (tmt-80) REVERT: B 173 HIS cc_start: 0.6508 (OUTLIER) cc_final: 0.5535 (m-70) REVERT: B 272 LYS cc_start: 0.7357 (tppp) cc_final: 0.6881 (ttpp) REVERT: B 279 GLU cc_start: 0.8413 (tt0) cc_final: 0.8059 (tt0) REVERT: B 283 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8605 (mttt) REVERT: B 331 MET cc_start: 0.7125 (ttp) cc_final: 0.6877 (ttp) REVERT: B 364 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7102 (mm-30) REVERT: B 380 LYS cc_start: 0.7355 (mmtp) cc_final: 0.6921 (mmmt) REVERT: B 399 ARG cc_start: 0.8397 (mtm180) cc_final: 0.7567 (tpt170) REVERT: B 410 SER cc_start: 0.9212 (OUTLIER) cc_final: 0.8753 (m) REVERT: C 51 MET cc_start: 0.8484 (tpp) cc_final: 0.8259 (mmt) REVERT: C 126 ARG cc_start: 0.7183 (mtm110) cc_final: 0.6379 (mtm110) REVERT: C 131 ARG cc_start: 0.7720 (tpt-90) cc_final: 0.6123 (tmt-80) REVERT: C 173 HIS cc_start: 0.6521 (OUTLIER) cc_final: 0.5520 (m-70) REVERT: C 272 LYS cc_start: 0.7357 (tppp) cc_final: 0.6869 (ttpp) REVERT: C 279 GLU cc_start: 0.8418 (tt0) cc_final: 0.8062 (tt0) REVERT: C 283 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8598 (mttt) REVERT: C 331 MET cc_start: 0.7120 (ttp) cc_final: 0.6872 (ttp) REVERT: C 364 GLU cc_start: 0.7283 (mt-10) cc_final: 0.7029 (mm-30) REVERT: C 380 LYS cc_start: 0.7352 (mmtp) cc_final: 0.6923 (mmmt) REVERT: C 399 ARG cc_start: 0.8389 (mtm180) cc_final: 0.7576 (tpt170) REVERT: C 410 SER cc_start: 0.9220 (OUTLIER) cc_final: 0.8757 (m) REVERT: D 51 MET cc_start: 0.8445 (tpp) cc_final: 0.8212 (mmt) REVERT: D 126 ARG cc_start: 0.7165 (mtm110) cc_final: 0.6360 (mtm110) REVERT: D 131 ARG cc_start: 0.7725 (tpt-90) cc_final: 0.6120 (tmt-80) REVERT: D 173 HIS cc_start: 0.6434 (OUTLIER) cc_final: 0.5470 (m-70) REVERT: D 272 LYS cc_start: 0.7346 (tppp) cc_final: 0.6882 (ttpp) REVERT: D 283 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8615 (mttt) REVERT: D 331 MET cc_start: 0.7129 (ttp) cc_final: 0.6881 (ttp) REVERT: D 364 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7101 (mm-30) REVERT: D 380 LYS cc_start: 0.7378 (mmtp) cc_final: 0.6944 (mmmt) REVERT: D 399 ARG cc_start: 0.8406 (mtm180) cc_final: 0.7590 (tpt170) REVERT: D 410 SER cc_start: 0.9213 (OUTLIER) cc_final: 0.8751 (m) outliers start: 26 outliers final: 8 residues processed: 178 average time/residue: 1.3420 time to fit residues: 259.2619 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 : 1.457 ------------------------------------------------------------------------------- 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 345 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 173 HIS 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 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 C residue 410 SER Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 283 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 0.0370 chunk 109 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.160743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.117303 restraints weight = 12081.106| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.59 r_work: 0.3049 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2352 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= 0.109 Angle : 0.392 4.890 16596 Z= 0.217 Chirality : 0.034 0.132 1988 Planarity : 0.003 0.026 2032 Dihedral : 3.352 13.004 1656 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.45 % Allowed : 20.64 % Favored : 77.91 % 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: 3.69 (0.21), residues: 1504 helix: 2.97 (0.13), residues: 1264 sheet: 0.76 (0.50), residues: 48 loop : -1.15 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 154 HIS 0.001 0.000 HIS B 306 PHE 0.009 0.001 PHE A 11 TYR 0.006 0.001 TYR D 96 ARG 0.001 0.000 ARG C 367 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 1068) hydrogen bonds : angle 3.75943 ( 3204) covalent geometry : bond 0.00217 (12236) covalent geometry : angle 0.39183 (16596) ********************** 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 187 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 1.297 Fit side-chains REVERT: A 51 MET cc_start: 0.8508 (tpp) cc_final: 0.8296 (mmt) REVERT: A 126 ARG cc_start: 0.7304 (mtm110) cc_final: 0.6540 (mtm110) REVERT: A 131 ARG cc_start: 0.7832 (tpt-90) cc_final: 0.6276 (tmt-80) REVERT: A 173 HIS cc_start: 0.6562 (OUTLIER) cc_final: 0.5586 (m-70) REVERT: A 272 LYS cc_start: 0.7405 (tppp) cc_final: 0.6965 (ttpp) REVERT: A 279 GLU cc_start: 0.8456 (tt0) cc_final: 0.8118 (tt0) REVERT: A 283 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8656 (mttt) REVERT: A 331 MET cc_start: 0.7250 (ttp) cc_final: 0.7005 (ttp) REVERT: A 364 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7216 (mm-30) REVERT: A 380 LYS cc_start: 0.7450 (mmtp) cc_final: 0.7028 (mmmt) REVERT: A 399 ARG cc_start: 0.8424 (mtm180) cc_final: 0.7649 (tpt170) REVERT: A 410 SER cc_start: 0.9231 (OUTLIER) cc_final: 0.8778 (m) REVERT: B 51 MET cc_start: 0.8498 (tpp) cc_final: 0.8286 (mmt) REVERT: B 126 ARG cc_start: 0.7338 (mtm110) cc_final: 0.6556 (mtm110) REVERT: B 131 ARG cc_start: 0.7829 (tpt-90) cc_final: 0.6279 (tmt-80) REVERT: B 173 HIS cc_start: 0.6535 (OUTLIER) cc_final: 0.5549 (m-70) REVERT: B 272 LYS cc_start: 0.7399 (tppp) cc_final: 0.6966 (ttpp) REVERT: B 279 GLU cc_start: 0.8447 (tt0) cc_final: 0.8111 (tt0) REVERT: B 283 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8660 (mttt) REVERT: B 331 MET cc_start: 0.7260 (ttp) cc_final: 0.7016 (ttp) REVERT: B 364 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7224 (mm-30) REVERT: B 380 LYS cc_start: 0.7452 (mmtp) cc_final: 0.7029 (mmmt) REVERT: B 399 ARG cc_start: 0.8424 (mtm180) cc_final: 0.7648 (tpt170) REVERT: B 410 SER cc_start: 0.9234 (OUTLIER) cc_final: 0.8783 (m) REVERT: C 51 MET cc_start: 0.8507 (tpp) cc_final: 0.8299 (mmt) REVERT: C 126 ARG cc_start: 0.7325 (mtm110) cc_final: 0.6545 (mtm110) REVERT: C 131 ARG cc_start: 0.7821 (tpt-90) cc_final: 0.6270 (tmt-80) REVERT: C 173 HIS cc_start: 0.6563 (OUTLIER) cc_final: 0.5583 (m-70) REVERT: C 272 LYS cc_start: 0.7417 (tppp) cc_final: 0.6975 (ttpp) REVERT: C 279 GLU cc_start: 0.8447 (tt0) cc_final: 0.8109 (tt0) REVERT: C 283 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8654 (mttt) REVERT: C 331 MET cc_start: 0.7251 (ttp) cc_final: 0.7009 (ttp) REVERT: C 364 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7150 (mm-30) REVERT: C 380 LYS cc_start: 0.7454 (mmtp) cc_final: 0.7036 (mmmt) REVERT: C 399 ARG cc_start: 0.8428 (mtm180) cc_final: 0.7657 (tpt170) REVERT: C 410 SER cc_start: 0.9233 (OUTLIER) cc_final: 0.8780 (m) REVERT: D 51 MET cc_start: 0.8494 (tpp) cc_final: 0.8278 (mmt) REVERT: D 126 ARG cc_start: 0.7265 (mtm110) cc_final: 0.6474 (mtm110) REVERT: D 131 ARG cc_start: 0.7821 (tpt-90) cc_final: 0.6263 (tmt-80) REVERT: D 173 HIS cc_start: 0.6553 (OUTLIER) cc_final: 0.5572 (m-70) REVERT: D 272 LYS cc_start: 0.7416 (tppp) cc_final: 0.6973 (ttpp) REVERT: D 283 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8666 (mttt) REVERT: D 331 MET cc_start: 0.7263 (ttp) cc_final: 0.7020 (ttp) REVERT: D 364 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7219 (mm-30) REVERT: D 380 LYS cc_start: 0.7441 (mmtp) cc_final: 0.7026 (mmmt) REVERT: D 399 ARG cc_start: 0.8430 (mtm180) cc_final: 0.7666 (tpt170) REVERT: D 410 SER cc_start: 0.9226 (OUTLIER) cc_final: 0.8776 (m) outliers start: 19 outliers final: 5 residues processed: 183 average time/residue: 1.2795 time to fit residues: 253.1722 Evaluate side-chains 173 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 A residue 410 SER Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER 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 C residue 410 SER Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 105 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.159153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.115621 restraints weight = 11986.952| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.60 r_work: 0.3073 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12236 Z= 0.133 Angle : 0.413 5.015 16596 Z= 0.227 Chirality : 0.035 0.132 1988 Planarity : 0.003 0.026 2032 Dihedral : 3.417 13.279 1656 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.14 % Allowed : 19.88 % Favored : 77.98 % 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: 3.56 (0.21), residues: 1504 helix: 2.89 (0.13), residues: 1264 sheet: 0.70 (0.49), residues: 48 loop : -1.23 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 154 HIS 0.001 0.000 HIS A 349 PHE 0.009 0.001 PHE A 11 TYR 0.007 0.001 TYR B 175 ARG 0.001 0.000 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 1068) hydrogen bonds : angle 3.81217 ( 3204) covalent geometry : bond 0.00286 (12236) covalent geometry : angle 0.41339 (16596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9540.26 seconds wall clock time: 167 minutes 27.44 seconds (10047.44 seconds total)