Starting phenix.real_space_refine on Fri Oct 23 00:27:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f5x_31469/10_2026/7f5x_31469.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f5x_31469/10_2026/7f5x_31469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7f5x_31469/10_2026/7f5x_31469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f5x_31469/10_2026/7f5x_31469.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f5x_31469/10_2026/7f5x_31469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f5x_31469/10_2026/7f5x_31469.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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 52 5.16 5 C 4572 2.51 5 N 1240 2.21 5 O 1380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7244 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1801 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 3 Chain: "B" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1801 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 3 Chain: "C" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1801 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 3 Chain: "D" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1801 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 3 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 1.57, per 1000 atoms: 0.22 Number of scatterers: 7244 At special positions: 0 Unit cell: (109.18, 87.98, 75.26, 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 52 16.00 O 1380 8.00 N 1240 7.00 C 4572 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 451.1 milliseconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 12 sheets defined 49.6% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 49 through 56 removed outlier: 4.119A pdb=" N LYS A 54 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 56 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 93 removed outlier: 3.521A pdb=" N LEU A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.541A pdb=" N GLY A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.807A pdb=" N SER A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 163 Processing helix chain 'A' and resid 174 through 179 Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 234 through 245 Processing helix chain 'A' and resid 298 through 308 Processing helix chain 'A' and resid 321 through 329 removed outlier: 3.508A pdb=" N GLY A 328 " --> pdb=" O LYS A 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 56 removed outlier: 4.119A pdb=" N LYS B 54 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA B 56 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 93 removed outlier: 3.521A pdb=" N LEU B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 114 removed outlier: 3.541A pdb=" N GLY B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 122 removed outlier: 3.807A pdb=" N SER B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 163 Processing helix chain 'B' and resid 174 through 179 Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 234 through 245 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 321 through 329 removed outlier: 3.508A pdb=" N GLY B 328 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 56 removed outlier: 4.119A pdb=" N LYS C 54 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA C 56 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 93 removed outlier: 3.521A pdb=" N LEU C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 114 removed outlier: 3.541A pdb=" N GLY C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.807A pdb=" N SER C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 163 Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 180 through 196 Processing helix chain 'C' and resid 234 through 245 Processing helix chain 'C' and resid 298 through 308 Processing helix chain 'C' and resid 321 through 329 removed outlier: 3.508A pdb=" N GLY C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 56 removed outlier: 4.119A pdb=" N LYS D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA D 56 " --> pdb=" O LEU D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 93 removed outlier: 3.521A pdb=" N LEU D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 114 removed outlier: 3.541A pdb=" N GLY D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 122 removed outlier: 3.807A pdb=" N SER D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 163 Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 180 through 196 Processing helix chain 'D' and resid 234 through 245 Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 321 through 329 removed outlier: 3.508A pdb=" N GLY D 328 " --> pdb=" O LYS D 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 173 removed outlier: 3.645A pdb=" N ALA A 169 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 250 removed outlier: 6.226A pdb=" N LEU A 249 " --> pdb=" O VAL A 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 273 through 274 Processing sheet with id=AA4, first strand: chain 'B' and resid 168 through 173 removed outlier: 3.645A pdb=" N ALA B 169 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 248 through 250 removed outlier: 6.226A pdb=" N LEU B 249 " --> pdb=" O VAL B 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 273 through 274 Processing sheet with id=AA7, first strand: chain 'C' and resid 168 through 173 removed outlier: 3.645A pdb=" N ALA C 169 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 248 through 250 removed outlier: 6.226A pdb=" N LEU C 249 " --> pdb=" O VAL C 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 274 Processing sheet with id=AB1, first strand: chain 'D' and resid 168 through 173 removed outlier: 3.645A pdb=" N ALA D 169 " --> pdb=" O VAL D 200 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 248 through 250 removed outlier: 6.226A pdb=" N LEU D 249 " --> pdb=" O VAL D 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 273 through 274 312 hydrogen bonds defined for protein. 864 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: 0.99 Time building geometry restraints manager: 0.89 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: 2396 1.34 - 1.46: 1168 1.46 - 1.57: 3676 1.57 - 1.69: 0 1.69 - 1.80: 92 Bond restraints: 7332 Sorted by residual: bond pdb=" CG GGL D 801 " pdb=" CD GGL D 801 " ideal model delta sigma weight residual 1.544 1.516 0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" CG GGL B 801 " pdb=" CD GGL B 801 " ideal model delta sigma weight residual 1.544 1.516 0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" CG GGL C 801 " pdb=" CD GGL C 801 " ideal model delta sigma weight residual 1.544 1.516 0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" CG GGL A 801 " pdb=" CD GGL A 801 " ideal model delta sigma weight residual 1.544 1.516 0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" N ASN A 233 " pdb=" CA ASN A 233 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.82e+00 ... (remaining 7327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 9700 1.73 - 3.47: 152 3.47 - 5.20: 24 5.20 - 6.93: 4 6.93 - 8.66: 4 Bond angle restraints: 9884 Sorted by residual: angle pdb=" N ASN B 233 " pdb=" CA ASN B 233 " pdb=" C ASN B 233 " ideal model delta sigma weight residual 110.80 119.46 -8.66 2.13e+00 2.20e-01 1.65e+01 angle pdb=" N ASN D 233 " pdb=" CA ASN D 233 " pdb=" C ASN D 233 " ideal model delta sigma weight residual 110.80 119.46 -8.66 2.13e+00 2.20e-01 1.65e+01 angle pdb=" N ASN C 233 " pdb=" CA ASN C 233 " pdb=" C ASN C 233 " ideal model delta sigma weight residual 110.80 119.46 -8.66 2.13e+00 2.20e-01 1.65e+01 angle pdb=" N ASN A 233 " pdb=" CA ASN A 233 " pdb=" C ASN A 233 " ideal model delta sigma weight residual 110.80 119.46 -8.66 2.13e+00 2.20e-01 1.65e+01 angle pdb=" N THR B 46 " pdb=" CA THR B 46 " pdb=" C THR B 46 " ideal model delta sigma weight residual 114.56 110.16 4.40 1.27e+00 6.20e-01 1.20e+01 ... (remaining 9879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3880 17.98 - 35.96: 466 35.96 - 53.95: 110 53.95 - 71.93: 8 71.93 - 89.91: 28 Dihedral angle restraints: 4492 sinusoidal: 1772 harmonic: 2720 Sorted by residual: dihedral pdb=" CA ASP D 72 " pdb=" C ASP D 72 " pdb=" N ASN D 73 " pdb=" CA ASN D 73 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ASP B 72 " pdb=" C ASP B 72 " pdb=" N ASN B 73 " pdb=" CA ASN B 73 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ASP C 72 " pdb=" C ASP C 72 " pdb=" N ASN C 73 " pdb=" CA ASN C 73 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1080 0.073 - 0.146: 92 0.146 - 0.219: 0 0.219 - 0.291: 0 0.291 - 0.364: 4 Chirality restraints: 1176 Sorted by residual: chirality pdb=" CA ASN B 233 " pdb=" N ASN B 233 " pdb=" C ASN B 233 " pdb=" CB ASN B 233 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA ASN C 233 " pdb=" N ASN C 233 " pdb=" C ASN C 233 " pdb=" CB ASN C 233 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA ASN D 233 " pdb=" N ASN D 233 " pdb=" C ASN D 233 " pdb=" CB ASN D 233 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 1173 not shown) Planarity restraints: 1248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 175 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO B 176 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 176 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 176 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 175 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO D 176 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO D 176 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 176 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 175 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO A 176 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " 0.021 5.00e-02 4.00e+02 ... (remaining 1245 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 56 2.50 - 3.10: 5416 3.10 - 3.70: 10246 3.70 - 4.30: 14236 4.30 - 4.90: 24798 Nonbonded interactions: 54752 Sorted by model distance: nonbonded pdb=" CE2 PHE B 108 " pdb=" OE1 GLN D 163 " model vdw 1.896 3.340 nonbonded pdb=" OE1 GLN A 163 " pdb=" CE2 PHE C 108 " model vdw 1.896 3.340 nonbonded pdb=" CE2 PHE A 108 " pdb=" OE1 GLN C 163 " model vdw 1.896 3.340 nonbonded pdb=" OE1 GLN B 163 " pdb=" CE2 PHE D 108 " model vdw 1.896 3.340 nonbonded pdb=" O ALA A 56 " pdb=" NH1 ARG A 96 " model vdw 2.259 3.120 ... (remaining 54747 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.730 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.011 0.415 7336 Z= 0.993 Angle : 0.612 8.663 9884 Z= 0.339 Chirality : 0.046 0.364 1176 Planarity : 0.004 0.037 1248 Dihedral : 17.455 89.911 2724 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.46 % Favored : 91.67 % Rotamer: Outliers : 6.15 % Allowed : 26.67 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.25), residues: 912 helix: -1.10 (0.21), residues: 412 sheet: -4.57 (0.32), residues: 164 loop : -2.37 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 308 TYR 0.004 0.001 TYR B 164 PHE 0.008 0.002 PHE D 161 TRP 0.008 0.001 TRP A 304 HIS 0.001 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 ( 7332) covalent geometry : angle 0.61171 / 0.34 ( 9884) hydrogen bonds : bond 0.15781 / 10.49 ( 312) hydrogen bonds : angle 5.98892 / 4.24 ( 864) Misc. bond : bond 0.41507 / 24.83 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 0.333 Fit side-chains REVERT: A 52 GLN cc_start: 0.8001 (mp10) cc_final: 0.7773 (mp10) REVERT: A 123 MET cc_start: 0.3887 (mmt) cc_final: 0.3123 (mtt) REVERT: A 154 MET cc_start: 0.8560 (mmm) cc_final: 0.8298 (mmm) REVERT: A 170 GLN cc_start: 0.8801 (tt0) cc_final: 0.8596 (tt0) REVERT: A 262 PRO cc_start: 0.7700 (Cg_exo) cc_final: 0.7435 (Cg_endo) REVERT: A 272 HIS cc_start: 0.8108 (m-70) cc_final: 0.7856 (m90) REVERT: B 52 GLN cc_start: 0.8002 (mp10) cc_final: 0.7773 (mp10) REVERT: B 123 MET cc_start: 0.3887 (mmt) cc_final: 0.3125 (mtt) REVERT: B 154 MET cc_start: 0.8561 (mmm) cc_final: 0.8298 (mmm) REVERT: B 170 GLN cc_start: 0.8804 (tt0) cc_final: 0.8595 (tt0) REVERT: B 262 PRO cc_start: 0.7701 (Cg_exo) cc_final: 0.7437 (Cg_endo) REVERT: B 272 HIS cc_start: 0.8105 (m-70) cc_final: 0.7856 (m90) REVERT: C 52 GLN cc_start: 0.8002 (mp10) cc_final: 0.7772 (mp10) REVERT: C 123 MET cc_start: 0.3886 (mmt) cc_final: 0.3123 (mtt) REVERT: C 154 MET cc_start: 0.8563 (mmm) cc_final: 0.8297 (mmm) REVERT: C 170 GLN cc_start: 0.8803 (tt0) cc_final: 0.8595 (tt0) REVERT: C 262 PRO cc_start: 0.7701 (Cg_exo) cc_final: 0.7438 (Cg_endo) REVERT: C 272 HIS cc_start: 0.8107 (m-70) cc_final: 0.7857 (m90) REVERT: D 52 GLN cc_start: 0.8002 (mp10) cc_final: 0.7773 (mp10) REVERT: D 123 MET cc_start: 0.3887 (mmt) cc_final: 0.3124 (mtt) REVERT: D 154 MET cc_start: 0.8561 (mmm) cc_final: 0.8300 (mmm) REVERT: D 170 GLN cc_start: 0.8803 (tt0) cc_final: 0.8597 (tt0) REVERT: D 262 PRO cc_start: 0.7700 (Cg_exo) cc_final: 0.7435 (Cg_endo) REVERT: D 272 HIS cc_start: 0.8108 (m-70) cc_final: 0.7856 (m90) outliers start: 48 outliers final: 40 residues processed: 256 average time/residue: 0.0646 time to fit residues: 23.8672 Evaluate side-chains 224 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 313 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.0170 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS A 186 ASN B 74 HIS B 186 ASN C 74 HIS C 186 ASN D 74 HIS D 186 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.179011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.142589 restraints weight = 8627.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.147533 restraints weight = 5206.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.150922 restraints weight = 3819.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.153169 restraints weight = 3120.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.154673 restraints weight = 2712.350| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7336 Z= 0.149 Angle : 0.529 5.071 9884 Z= 0.283 Chirality : 0.041 0.139 1176 Planarity : 0.004 0.042 1248 Dihedral : 9.093 50.764 1104 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.08 % Allowed : 31.28 % Favored : 65.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.27), residues: 912 helix: 0.11 (0.23), residues: 416 sheet: -4.04 (0.35), residues: 168 loop : -1.69 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 143 TYR 0.007 0.001 TYR A 55 PHE 0.009 0.002 PHE A 108 TRP 0.008 0.001 TRP B 304 HIS 0.006 0.002 HIS C 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 7332) covalent geometry : angle 0.52922 / 0.28 ( 9884) hydrogen bonds : bond 0.04976 / 3.21 ( 312) hydrogen bonds : angle 4.45663 / 3.12 ( 864) Misc. bond : bond 0.00030 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 228 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7484 (mm-30) REVERT: A 62 LYS cc_start: 0.8343 (tmtt) cc_final: 0.8012 (tptm) REVERT: A 76 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8443 (tm) REVERT: A 94 GLU cc_start: 0.8387 (tt0) cc_final: 0.8128 (tt0) REVERT: A 123 MET cc_start: 0.4130 (mmt) cc_final: 0.3296 (mtt) REVERT: A 170 GLN cc_start: 0.8840 (tt0) cc_final: 0.8599 (tt0) REVERT: A 262 PRO cc_start: 0.7779 (Cg_exo) cc_final: 0.7407 (Cg_endo) REVERT: A 272 HIS cc_start: 0.7993 (m-70) cc_final: 0.7694 (m90) REVERT: B 49 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7490 (mm-30) REVERT: B 62 LYS cc_start: 0.8336 (tmtt) cc_final: 0.8003 (tptm) REVERT: B 76 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8450 (tm) REVERT: B 94 GLU cc_start: 0.8379 (tt0) cc_final: 0.8121 (tt0) REVERT: B 123 MET cc_start: 0.4118 (mmt) cc_final: 0.3287 (mtt) REVERT: B 170 GLN cc_start: 0.8841 (tt0) cc_final: 0.8601 (tt0) REVERT: B 262 PRO cc_start: 0.7778 (Cg_exo) cc_final: 0.7406 (Cg_endo) REVERT: B 272 HIS cc_start: 0.8000 (m-70) cc_final: 0.7694 (m90) REVERT: C 49 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7493 (mm-30) REVERT: C 62 LYS cc_start: 0.8346 (tmtt) cc_final: 0.8037 (tptm) REVERT: C 76 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8448 (tm) REVERT: C 94 GLU cc_start: 0.8382 (tt0) cc_final: 0.8125 (tt0) REVERT: C 123 MET cc_start: 0.4129 (mmt) cc_final: 0.3296 (mtt) REVERT: C 170 GLN cc_start: 0.8844 (tt0) cc_final: 0.8600 (tt0) REVERT: C 262 PRO cc_start: 0.7779 (Cg_exo) cc_final: 0.7414 (Cg_endo) REVERT: C 272 HIS cc_start: 0.8008 (m-70) cc_final: 0.7700 (m90) REVERT: D 49 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7484 (mm-30) REVERT: D 62 LYS cc_start: 0.8340 (tmtt) cc_final: 0.8032 (tptm) REVERT: D 76 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8447 (tm) REVERT: D 94 GLU cc_start: 0.8382 (tt0) cc_final: 0.8121 (tt0) REVERT: D 123 MET cc_start: 0.4116 (mmt) cc_final: 0.3285 (mtt) REVERT: D 170 GLN cc_start: 0.8841 (tt0) cc_final: 0.8599 (tt0) REVERT: D 262 PRO cc_start: 0.7780 (Cg_exo) cc_final: 0.7431 (Cg_endo) REVERT: D 272 HIS cc_start: 0.7984 (m-70) cc_final: 0.7689 (m90) outliers start: 24 outliers final: 20 residues processed: 240 average time/residue: 0.0637 time to fit residues: 21.9289 Evaluate side-chains 224 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 254 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: [25, 72, 42, 24, 88, 19, 37, 68, 89, 23, 55] chunk 25 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS A 204 ASN B 74 HIS C 74 HIS D 74 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.172286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.135728 restraints weight = 8760.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.140255 restraints weight = 5397.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.143397 restraints weight = 4026.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.145400 restraints weight = 3331.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.146777 restraints weight = 2938.311| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 7336 Z= 0.288 Angle : 0.634 4.990 9884 Z= 0.339 Chirality : 0.044 0.143 1176 Planarity : 0.004 0.045 1248 Dihedral : 7.967 57.494 1056 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.89 % Favored : 91.67 % Rotamer: Outliers : 7.56 % Allowed : 26.79 % Favored : 65.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.27), residues: 912 helix: 0.05 (0.23), residues: 444 sheet: -4.05 (0.34), residues: 168 loop : -2.05 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 308 TYR 0.005 0.001 TYR A 55 PHE 0.009 0.002 PHE A 161 TRP 0.012 0.002 TRP D 304 HIS 0.007 0.002 HIS D 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.29 ( 7332) covalent geometry : angle 0.63360 / 0.34 ( 9884) hydrogen bonds : bond 0.06797 / 4.30 ( 312) hydrogen bonds : angle 4.46015 / 3.13 ( 864) Misc. bond : bond 0.00065 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 212 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.8630 (tmtt) cc_final: 0.8226 (tptm) REVERT: A 76 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8453 (tm) REVERT: A 123 MET cc_start: 0.4272 (mmt) cc_final: 0.3466 (mtt) REVERT: A 154 MET cc_start: 0.8584 (mmm) cc_final: 0.8283 (mmm) REVERT: A 170 GLN cc_start: 0.8902 (tt0) cc_final: 0.8588 (tt0) REVERT: A 252 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7644 (mmm) REVERT: A 262 PRO cc_start: 0.7831 (Cg_exo) cc_final: 0.7603 (Cg_endo) REVERT: A 272 HIS cc_start: 0.8084 (m-70) cc_final: 0.7808 (m90) REVERT: B 62 LYS cc_start: 0.8623 (tmtt) cc_final: 0.8221 (tptm) REVERT: B 76 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8466 (tm) REVERT: B 123 MET cc_start: 0.4261 (mmt) cc_final: 0.3457 (mtt) REVERT: B 154 MET cc_start: 0.8582 (mmm) cc_final: 0.8274 (mmm) REVERT: B 170 GLN cc_start: 0.8907 (tt0) cc_final: 0.8590 (tt0) REVERT: B 252 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7640 (mmm) REVERT: B 262 PRO cc_start: 0.7838 (Cg_exo) cc_final: 0.7616 (Cg_endo) REVERT: B 272 HIS cc_start: 0.8073 (m-70) cc_final: 0.7804 (m90) REVERT: C 62 LYS cc_start: 0.8631 (tmtt) cc_final: 0.8228 (tptm) REVERT: C 76 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8459 (tm) REVERT: C 123 MET cc_start: 0.4274 (mmt) cc_final: 0.3470 (mtt) REVERT: C 154 MET cc_start: 0.8585 (mmm) cc_final: 0.8276 (mmm) REVERT: C 170 GLN cc_start: 0.8902 (tt0) cc_final: 0.8584 (tt0) REVERT: C 252 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7638 (mmm) REVERT: C 262 PRO cc_start: 0.7836 (Cg_exo) cc_final: 0.7610 (Cg_endo) REVERT: C 272 HIS cc_start: 0.8083 (m-70) cc_final: 0.7814 (m90) REVERT: D 62 LYS cc_start: 0.8627 (tmtt) cc_final: 0.8225 (tptm) REVERT: D 76 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8467 (tm) REVERT: D 123 MET cc_start: 0.4263 (mmt) cc_final: 0.3458 (mtt) REVERT: D 154 MET cc_start: 0.8582 (mmm) cc_final: 0.8277 (mmm) REVERT: D 170 GLN cc_start: 0.8904 (tt0) cc_final: 0.8589 (tt0) REVERT: D 252 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7641 (mmm) REVERT: D 262 PRO cc_start: 0.7835 (Cg_exo) cc_final: 0.7611 (Cg_endo) REVERT: D 272 HIS cc_start: 0.8069 (m-70) cc_final: 0.7804 (m90) outliers start: 59 outliers final: 35 residues processed: 255 average time/residue: 0.0789 time to fit residues: 27.3132 Evaluate side-chains 271 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 228 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 254 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: [38, 77, 65, 87, 4, 51, 54, 14, 29, 20, 44] chunk 38 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS B 74 HIS C 74 HIS D 74 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.174510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.136537 restraints weight = 8669.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.141568 restraints weight = 5274.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.145061 restraints weight = 3889.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.147304 restraints weight = 3186.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.148978 restraints weight = 2785.407| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7336 Z= 0.169 Angle : 0.547 5.206 9884 Z= 0.297 Chirality : 0.041 0.146 1176 Planarity : 0.004 0.047 1248 Dihedral : 7.452 57.813 1054 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.49 % Allowed : 30.90 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.28), residues: 912 helix: 0.68 (0.24), residues: 416 sheet: -3.90 (0.33), residues: 168 loop : -1.63 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 330 TYR 0.004 0.001 TYR A 55 PHE 0.006 0.002 PHE D 108 TRP 0.007 0.001 TRP A 304 HIS 0.008 0.002 HIS C 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 ( 7332) covalent geometry : angle 0.54683 / 0.30 ( 9884) hydrogen bonds : bond 0.05169 / 3.30 ( 312) hydrogen bonds : angle 4.25886 / 2.98 ( 864) Misc. bond : bond 0.00034 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7575 (mm-30) REVERT: A 62 LYS cc_start: 0.8497 (tmtt) cc_final: 0.8267 (tptm) REVERT: A 94 GLU cc_start: 0.8403 (tt0) cc_final: 0.8130 (tt0) REVERT: A 123 MET cc_start: 0.4166 (mmt) cc_final: 0.3385 (mtt) REVERT: A 170 GLN cc_start: 0.8855 (tt0) cc_final: 0.8542 (tt0) REVERT: A 186 ASN cc_start: 0.8752 (m-40) cc_final: 0.8369 (m110) REVERT: A 262 PRO cc_start: 0.7799 (Cg_exo) cc_final: 0.7465 (Cg_endo) REVERT: A 272 HIS cc_start: 0.7889 (m-70) cc_final: 0.7663 (m90) REVERT: B 49 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7568 (mm-30) REVERT: B 62 LYS cc_start: 0.8487 (tmtt) cc_final: 0.8266 (tptm) REVERT: B 94 GLU cc_start: 0.8397 (tt0) cc_final: 0.8124 (tt0) REVERT: B 123 MET cc_start: 0.4151 (mmt) cc_final: 0.3376 (mtt) REVERT: B 170 GLN cc_start: 0.8859 (tt0) cc_final: 0.8543 (tt0) REVERT: B 186 ASN cc_start: 0.8745 (m-40) cc_final: 0.8368 (m110) REVERT: B 262 PRO cc_start: 0.7799 (Cg_exo) cc_final: 0.7456 (Cg_endo) REVERT: B 272 HIS cc_start: 0.7889 (m-70) cc_final: 0.7663 (m90) REVERT: C 49 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7574 (mm-30) REVERT: C 62 LYS cc_start: 0.8499 (tmtt) cc_final: 0.8273 (tptm) REVERT: C 94 GLU cc_start: 0.8398 (tt0) cc_final: 0.8126 (tt0) REVERT: C 123 MET cc_start: 0.4211 (mmt) cc_final: 0.3409 (mtt) REVERT: C 170 GLN cc_start: 0.8858 (tt0) cc_final: 0.8534 (tt0) REVERT: C 186 ASN cc_start: 0.8745 (m-40) cc_final: 0.8364 (m110) REVERT: C 262 PRO cc_start: 0.7803 (Cg_exo) cc_final: 0.7469 (Cg_endo) REVERT: C 272 HIS cc_start: 0.7888 (m-70) cc_final: 0.7664 (m90) REVERT: D 49 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7572 (mm-30) REVERT: D 62 LYS cc_start: 0.8492 (tmtt) cc_final: 0.8265 (tptm) REVERT: D 94 GLU cc_start: 0.8398 (tt0) cc_final: 0.8128 (tt0) REVERT: D 123 MET cc_start: 0.4147 (mmt) cc_final: 0.3370 (mtt) REVERT: D 170 GLN cc_start: 0.8855 (tt0) cc_final: 0.8540 (tt0) REVERT: D 186 ASN cc_start: 0.8744 (m-40) cc_final: 0.8365 (m110) REVERT: D 262 PRO cc_start: 0.7804 (Cg_exo) cc_final: 0.7483 (Cg_endo) REVERT: D 272 HIS cc_start: 0.7883 (m-70) cc_final: 0.7658 (m90) outliers start: 35 outliers final: 19 residues processed: 247 average time/residue: 0.0736 time to fit residues: 25.0785 Evaluate side-chains 211 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 254 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: [90, 86, 67, 44, 63, 13, 83, 27, 84, 39, 79] chunk 90 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.175141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.136989 restraints weight = 8647.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.142127 restraints weight = 5201.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.145683 restraints weight = 3825.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.148014 restraints weight = 3127.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.149655 restraints weight = 2735.169| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7336 Z= 0.166 Angle : 0.523 5.220 9884 Z= 0.287 Chirality : 0.041 0.147 1176 Planarity : 0.004 0.046 1248 Dihedral : 6.643 58.304 1042 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.00 % Allowed : 30.38 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.28), residues: 912 helix: 0.96 (0.25), residues: 416 sheet: -3.78 (0.33), residues: 168 loop : -1.62 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 330 TYR 0.003 0.001 TYR D 55 PHE 0.006 0.001 PHE D 108 TRP 0.007 0.001 TRP C 304 HIS 0.006 0.002 HIS D 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 ( 7332) covalent geometry : angle 0.52307 / 0.29 ( 9884) hydrogen bonds : bond 0.04976 / 3.18 ( 312) hydrogen bonds : angle 4.08270 / 2.86 ( 864) Misc. bond : bond 0.00036 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.8413 (tmtt) cc_final: 0.7972 (tptp) REVERT: A 123 MET cc_start: 0.4199 (mmt) cc_final: 0.3397 (mtt) REVERT: A 161 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: A 170 GLN cc_start: 0.8872 (tt0) cc_final: 0.8555 (tt0) REVERT: A 186 ASN cc_start: 0.8727 (m-40) cc_final: 0.8348 (m110) REVERT: A 262 PRO cc_start: 0.7770 (Cg_exo) cc_final: 0.7514 (Cg_endo) REVERT: B 62 LYS cc_start: 0.8402 (tmtt) cc_final: 0.7963 (tptp) REVERT: B 123 MET cc_start: 0.4190 (mmt) cc_final: 0.3395 (mtt) REVERT: B 161 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.8199 (m-80) REVERT: B 170 GLN cc_start: 0.8875 (tt0) cc_final: 0.8555 (tt0) REVERT: B 186 ASN cc_start: 0.8721 (m-40) cc_final: 0.8344 (m110) REVERT: B 262 PRO cc_start: 0.7769 (Cg_exo) cc_final: 0.7505 (Cg_endo) REVERT: C 62 LYS cc_start: 0.8409 (tmtt) cc_final: 0.7964 (tptp) REVERT: C 123 MET cc_start: 0.4320 (mmt) cc_final: 0.3501 (mtt) REVERT: C 161 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8194 (m-80) REVERT: C 170 GLN cc_start: 0.8881 (tt0) cc_final: 0.8556 (tt0) REVERT: C 186 ASN cc_start: 0.8724 (m-40) cc_final: 0.8344 (m110) REVERT: C 262 PRO cc_start: 0.7771 (Cg_exo) cc_final: 0.7509 (Cg_endo) REVERT: C 272 HIS cc_start: 0.7841 (m-70) cc_final: 0.7639 (m90) REVERT: D 62 LYS cc_start: 0.8403 (tmtt) cc_final: 0.7961 (tptp) REVERT: D 123 MET cc_start: 0.4195 (mmt) cc_final: 0.3395 (mtt) REVERT: D 161 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8195 (m-80) REVERT: D 170 GLN cc_start: 0.8874 (tt0) cc_final: 0.8554 (tt0) REVERT: D 186 ASN cc_start: 0.8722 (m-40) cc_final: 0.8344 (m110) REVERT: D 262 PRO cc_start: 0.7772 (Cg_exo) cc_final: 0.7515 (Cg_endo) outliers start: 39 outliers final: 31 residues processed: 219 average time/residue: 0.0656 time to fit residues: 20.4875 Evaluate side-chains 252 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 161 PHE Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 161 PHE Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 254 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: [25, 12, 58, 70, 2, 85, 79, 87, 28, 86, 78] chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.179201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.142843 restraints weight = 8606.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.147887 restraints weight = 5132.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.151351 restraints weight = 3729.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.153651 restraints weight = 3026.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.155021 restraints weight = 2623.259| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7336 Z= 0.157 Angle : 0.517 5.246 9884 Z= 0.285 Chirality : 0.040 0.144 1176 Planarity : 0.004 0.045 1248 Dihedral : 6.530 58.077 1042 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.51 % Allowed : 29.36 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.28), residues: 912 helix: 1.11 (0.24), residues: 416 sheet: -3.74 (0.33), residues: 168 loop : -1.53 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 330 TYR 0.003 0.001 TYR A 55 PHE 0.006 0.001 PHE D 108 TRP 0.007 0.001 TRP D 304 HIS 0.007 0.002 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 7332) covalent geometry : angle 0.51730 / 0.29 ( 9884) hydrogen bonds : bond 0.04771 / 3.05 ( 312) hydrogen bonds : angle 4.03503 / 2.82 ( 864) Misc. bond : bond 0.00021 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8407 (tt0) cc_final: 0.8152 (tt0) REVERT: A 116 GLU cc_start: 0.8450 (mp0) cc_final: 0.7786 (mp0) REVERT: A 123 MET cc_start: 0.4267 (mmt) cc_final: 0.3417 (mtt) REVERT: A 163 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8594 (tp40) REVERT: A 170 GLN cc_start: 0.8874 (tt0) cc_final: 0.8619 (tt0) REVERT: A 186 ASN cc_start: 0.8712 (m-40) cc_final: 0.8308 (m110) REVERT: A 262 PRO cc_start: 0.7782 (Cg_exo) cc_final: 0.7464 (Cg_endo) REVERT: B 94 GLU cc_start: 0.8400 (tt0) cc_final: 0.8144 (tt0) REVERT: B 116 GLU cc_start: 0.8451 (mp0) cc_final: 0.7785 (mp0) REVERT: B 123 MET cc_start: 0.4264 (mmt) cc_final: 0.3417 (mtt) REVERT: B 163 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8593 (tp40) REVERT: B 170 GLN cc_start: 0.8881 (tt0) cc_final: 0.8623 (tt0) REVERT: B 186 ASN cc_start: 0.8709 (m-40) cc_final: 0.8310 (m110) REVERT: B 262 PRO cc_start: 0.7771 (Cg_exo) cc_final: 0.7447 (Cg_endo) REVERT: C 94 GLU cc_start: 0.8404 (tt0) cc_final: 0.8148 (tt0) REVERT: C 116 GLU cc_start: 0.8450 (mp0) cc_final: 0.7785 (mp0) REVERT: C 123 MET cc_start: 0.4275 (mmt) cc_final: 0.3427 (mtt) REVERT: C 163 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8594 (tp40) REVERT: C 170 GLN cc_start: 0.8883 (tt0) cc_final: 0.8541 (tt0) REVERT: C 186 ASN cc_start: 0.8707 (m-40) cc_final: 0.8304 (m110) REVERT: C 262 PRO cc_start: 0.7774 (Cg_exo) cc_final: 0.7449 (Cg_endo) REVERT: D 94 GLU cc_start: 0.8401 (tt0) cc_final: 0.8146 (tt0) REVERT: D 116 GLU cc_start: 0.8452 (mp0) cc_final: 0.7790 (mp0) REVERT: D 123 MET cc_start: 0.4264 (mmt) cc_final: 0.3416 (mtt) REVERT: D 163 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8595 (tp40) REVERT: D 170 GLN cc_start: 0.8881 (tt0) cc_final: 0.8543 (tt0) REVERT: D 186 ASN cc_start: 0.8703 (m-40) cc_final: 0.8305 (m110) REVERT: D 262 PRO cc_start: 0.7774 (Cg_exo) cc_final: 0.7456 (Cg_endo) outliers start: 43 outliers final: 35 residues processed: 256 average time/residue: 0.0724 time to fit residues: 25.7706 Evaluate side-chains 247 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 254 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: [72, 31, 7, 65, 21, 69, 52, 25, 11, 83, 64] chunk 72 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.172497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.135991 restraints weight = 8747.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.140658 restraints weight = 5279.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.143869 restraints weight = 3904.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.145941 restraints weight = 3188.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.147186 restraints weight = 2790.711| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 7336 Z= 0.289 Angle : 0.644 5.095 9884 Z= 0.350 Chirality : 0.043 0.141 1176 Planarity : 0.005 0.048 1248 Dihedral : 6.954 59.664 1042 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 7.82 % Allowed : 27.56 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.28), residues: 912 helix: 0.99 (0.25), residues: 416 sheet: -3.81 (0.33), residues: 168 loop : -1.58 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 308 TYR 0.005 0.001 TYR A 157 PHE 0.008 0.002 PHE D 188 TRP 0.012 0.002 TRP B 304 HIS 0.006 0.002 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.29 ( 7332) covalent geometry : angle 0.64411 / 0.35 ( 9884) hydrogen bonds : bond 0.06535 / 4.13 ( 312) hydrogen bonds : angle 4.28857 / 3.01 ( 864) Misc. bond : bond 0.00049 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 220 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8425 (tt0) cc_final: 0.8121 (tt0) REVERT: A 123 MET cc_start: 0.4013 (mmt) cc_final: 0.3283 (mtt) REVERT: A 154 MET cc_start: 0.8594 (mmm) cc_final: 0.8231 (mmm) REVERT: A 161 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8226 (m-80) REVERT: A 170 GLN cc_start: 0.8929 (tt0) cc_final: 0.8594 (tt0) REVERT: A 262 PRO cc_start: 0.7822 (Cg_exo) cc_final: 0.7549 (Cg_endo) REVERT: B 94 GLU cc_start: 0.8417 (tt0) cc_final: 0.8131 (tt0) REVERT: B 123 MET cc_start: 0.3999 (mmt) cc_final: 0.3274 (mtt) REVERT: B 154 MET cc_start: 0.8597 (mmm) cc_final: 0.8221 (mmm) REVERT: B 161 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8224 (m-80) REVERT: B 170 GLN cc_start: 0.8935 (tt0) cc_final: 0.8598 (tt0) REVERT: B 262 PRO cc_start: 0.7827 (Cg_exo) cc_final: 0.7556 (Cg_endo) REVERT: C 54 LYS cc_start: 0.8709 (mttm) cc_final: 0.8509 (ptpp) REVERT: C 94 GLU cc_start: 0.8421 (tt0) cc_final: 0.8119 (tt0) REVERT: C 123 MET cc_start: 0.4010 (mmt) cc_final: 0.3282 (mtt) REVERT: C 154 MET cc_start: 0.8596 (mmm) cc_final: 0.8222 (mmm) REVERT: C 161 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8228 (m-80) REVERT: C 170 GLN cc_start: 0.8937 (tt0) cc_final: 0.8597 (tt0) REVERT: C 262 PRO cc_start: 0.7826 (Cg_exo) cc_final: 0.7549 (Cg_endo) REVERT: D 94 GLU cc_start: 0.8426 (tt0) cc_final: 0.8123 (tt0) REVERT: D 123 MET cc_start: 0.4000 (mmt) cc_final: 0.3273 (mtt) REVERT: D 154 MET cc_start: 0.8593 (mmm) cc_final: 0.8221 (mmm) REVERT: D 161 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8220 (m-80) REVERT: D 170 GLN cc_start: 0.8939 (tt0) cc_final: 0.8598 (tt0) REVERT: D 262 PRO cc_start: 0.7822 (Cg_exo) cc_final: 0.7552 (Cg_endo) outliers start: 61 outliers final: 51 residues processed: 263 average time/residue: 0.0759 time to fit residues: 27.1998 Evaluate side-chains 283 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 228 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 161 PHE Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 161 PHE Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 254 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: [59, 2, 85, 19, 17, 63, 45, 86, 28, 6, 91] chunk 59 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 86 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS B 74 HIS C 74 HIS D 74 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.179772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.143636 restraints weight = 8762.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.148785 restraints weight = 5169.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.152242 restraints weight = 3735.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.154590 restraints weight = 3013.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.156156 restraints weight = 2601.814| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7336 Z= 0.147 Angle : 0.539 5.300 9884 Z= 0.301 Chirality : 0.040 0.138 1176 Planarity : 0.004 0.045 1248 Dihedral : 6.578 58.863 1042 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.97 % Allowed : 31.54 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.29), residues: 912 helix: 1.15 (0.24), residues: 420 sheet: -3.64 (0.33), residues: 168 loop : -1.35 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 330 TYR 0.008 0.001 TYR D 55 PHE 0.006 0.001 PHE A 108 TRP 0.005 0.001 TRP C 304 HIS 0.009 0.002 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 7332) covalent geometry : angle 0.53939 / 0.30 ( 9884) hydrogen bonds : bond 0.04404 / 2.83 ( 312) hydrogen bonds : angle 4.13050 / 2.88 ( 864) Misc. bond : bond 0.00010 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.8554 (m-80) cc_final: 0.8297 (m-10) REVERT: A 62 LYS cc_start: 0.8347 (tmtt) cc_final: 0.7682 (tptm) REVERT: A 73 ASN cc_start: 0.7263 (t0) cc_final: 0.6660 (t0) REVERT: A 94 GLU cc_start: 0.8363 (tt0) cc_final: 0.8076 (tt0) REVERT: A 116 GLU cc_start: 0.8622 (mp0) cc_final: 0.7957 (mp0) REVERT: A 123 MET cc_start: 0.4191 (mmt) cc_final: 0.3361 (mtt) REVERT: A 150 GLN cc_start: 0.8314 (tp40) cc_final: 0.8065 (tp-100) REVERT: A 182 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8118 (mt-10) REVERT: A 186 ASN cc_start: 0.8564 (m-40) cc_final: 0.8196 (m110) REVERT: A 262 PRO cc_start: 0.7731 (Cg_exo) cc_final: 0.7466 (Cg_endo) REVERT: B 55 TYR cc_start: 0.8531 (m-80) cc_final: 0.8275 (m-10) REVERT: B 62 LYS cc_start: 0.8328 (tmtt) cc_final: 0.7667 (tptm) REVERT: B 73 ASN cc_start: 0.7258 (t0) cc_final: 0.6653 (t0) REVERT: B 94 GLU cc_start: 0.8348 (tt0) cc_final: 0.8061 (tt0) REVERT: B 116 GLU cc_start: 0.8621 (mp0) cc_final: 0.7958 (mp0) REVERT: B 123 MET cc_start: 0.4190 (mmt) cc_final: 0.3364 (mtt) REVERT: B 170 GLN cc_start: 0.8869 (tt0) cc_final: 0.8556 (tt0) REVERT: B 182 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8104 (mt-10) REVERT: B 186 ASN cc_start: 0.8558 (m-40) cc_final: 0.8187 (m110) REVERT: B 262 PRO cc_start: 0.7734 (Cg_exo) cc_final: 0.7472 (Cg_endo) REVERT: C 62 LYS cc_start: 0.8334 (tmtt) cc_final: 0.7670 (tptm) REVERT: C 73 ASN cc_start: 0.7299 (t0) cc_final: 0.6695 (t0) REVERT: C 94 GLU cc_start: 0.8361 (tt0) cc_final: 0.8078 (tt0) REVERT: C 116 GLU cc_start: 0.8626 (mp0) cc_final: 0.7958 (mp0) REVERT: C 123 MET cc_start: 0.4200 (mmt) cc_final: 0.3371 (mtt) REVERT: C 170 GLN cc_start: 0.8876 (tt0) cc_final: 0.8551 (tt0) REVERT: C 182 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8129 (mt-10) REVERT: C 186 ASN cc_start: 0.8559 (m-40) cc_final: 0.8184 (m110) REVERT: C 262 PRO cc_start: 0.7732 (Cg_exo) cc_final: 0.7467 (Cg_endo) REVERT: D 55 TYR cc_start: 0.8549 (m-80) cc_final: 0.8291 (m-10) REVERT: D 62 LYS cc_start: 0.8334 (tmtt) cc_final: 0.7673 (tptm) REVERT: D 73 ASN cc_start: 0.7258 (t0) cc_final: 0.6654 (t0) REVERT: D 94 GLU cc_start: 0.8355 (tt0) cc_final: 0.8073 (tt0) REVERT: D 116 GLU cc_start: 0.8603 (mp0) cc_final: 0.7943 (mp0) REVERT: D 123 MET cc_start: 0.4190 (mmt) cc_final: 0.3364 (mtt) REVERT: D 170 GLN cc_start: 0.8870 (tt0) cc_final: 0.8610 (tt0) REVERT: D 182 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8115 (mt-10) REVERT: D 186 ASN cc_start: 0.8563 (m-40) cc_final: 0.8188 (m110) REVERT: D 262 PRO cc_start: 0.7734 (Cg_exo) cc_final: 0.7474 (Cg_endo) outliers start: 31 outliers final: 31 residues processed: 252 average time/residue: 0.0698 time to fit residues: 24.9504 Evaluate side-chains 240 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 254 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: [20, 5, 7, 2, 47, 79, 29, 12, 81, 26, 72] chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.177345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.141117 restraints weight = 8732.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.146074 restraints weight = 5182.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.149452 restraints weight = 3784.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.151602 restraints weight = 3070.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.153260 restraints weight = 2674.966| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7336 Z= 0.170 Angle : 0.591 5.463 9884 Z= 0.322 Chirality : 0.040 0.139 1176 Planarity : 0.004 0.046 1248 Dihedral : 6.552 58.869 1042 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 5.00 % Allowed : 32.69 % Favored : 62.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.29), residues: 912 helix: 1.41 (0.25), residues: 420 sheet: -3.58 (0.33), residues: 168 loop : -1.23 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 330 TYR 0.008 0.001 TYR C 55 PHE 0.006 0.001 PHE A 108 TRP 0.008 0.001 TRP C 304 HIS 0.006 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 7332) covalent geometry : angle 0.59059 / 0.32 ( 9884) hydrogen bonds : bond 0.04856 / 3.10 ( 312) hydrogen bonds : angle 3.98953 / 2.79 ( 864) Misc. bond : bond 0.00024 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.8644 (mp0) cc_final: 0.7980 (mp0) REVERT: A 123 MET cc_start: 0.4198 (mmt) cc_final: 0.3374 (mtt) REVERT: A 170 GLN cc_start: 0.8881 (tt0) cc_final: 0.8597 (tt0) REVERT: A 186 ASN cc_start: 0.8563 (m-40) cc_final: 0.8162 (m110) REVERT: A 262 PRO cc_start: 0.7749 (Cg_exo) cc_final: 0.7464 (Cg_endo) REVERT: B 116 GLU cc_start: 0.8645 (mp0) cc_final: 0.7981 (mp0) REVERT: B 123 MET cc_start: 0.4199 (mmt) cc_final: 0.3376 (mtt) REVERT: B 170 GLN cc_start: 0.8885 (tt0) cc_final: 0.8549 (tt0) REVERT: B 186 ASN cc_start: 0.8550 (m-40) cc_final: 0.8158 (m110) REVERT: B 262 PRO cc_start: 0.7750 (Cg_exo) cc_final: 0.7465 (Cg_endo) REVERT: C 55 TYR cc_start: 0.8516 (m-80) cc_final: 0.8278 (m-10) REVERT: C 116 GLU cc_start: 0.8646 (mp0) cc_final: 0.7982 (mp0) REVERT: C 123 MET cc_start: 0.4209 (mmt) cc_final: 0.3382 (mtt) REVERT: C 170 GLN cc_start: 0.8878 (tt0) cc_final: 0.8528 (tt0) REVERT: C 186 ASN cc_start: 0.8554 (m-40) cc_final: 0.8159 (m110) REVERT: C 262 PRO cc_start: 0.7754 (Cg_exo) cc_final: 0.7469 (Cg_endo) REVERT: D 116 GLU cc_start: 0.8646 (mp0) cc_final: 0.7982 (mp0) REVERT: D 123 MET cc_start: 0.4209 (mmt) cc_final: 0.3384 (mtt) REVERT: D 170 GLN cc_start: 0.8896 (tt0) cc_final: 0.8544 (tt0) REVERT: D 186 ASN cc_start: 0.8556 (m-40) cc_final: 0.8159 (m110) REVERT: D 262 PRO cc_start: 0.7759 (Cg_exo) cc_final: 0.7475 (Cg_endo) outliers start: 39 outliers final: 39 residues processed: 225 average time/residue: 0.0674 time to fit residues: 21.3672 Evaluate side-chains 238 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 320 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: [32, 70, 42, 39, 43, 48, 5, 41, 63, 23, 59] chunk 32 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 0.0770 chunk 39 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 59 optimal weight: 0.0370 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 HIS C 74 HIS D 74 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.180997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.144371 restraints weight = 8739.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.149407 restraints weight = 5208.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.152951 restraints weight = 3800.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.154963 restraints weight = 3083.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.156889 restraints weight = 2702.256| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7336 Z= 0.144 Angle : 0.568 5.901 9884 Z= 0.313 Chirality : 0.040 0.138 1176 Planarity : 0.004 0.047 1248 Dihedral : 6.388 58.062 1042 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.00 % Allowed : 31.41 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.29), residues: 912 helix: 1.56 (0.25), residues: 420 sheet: -3.42 (0.33), residues: 168 loop : -1.10 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 330 TYR 0.004 0.000 TYR D 55 PHE 0.006 0.001 PHE A 108 TRP 0.006 0.001 TRP C 304 HIS 0.009 0.002 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 7332) covalent geometry : angle 0.56775 / 0.31 ( 9884) hydrogen bonds : bond 0.04220 / 2.71 ( 312) hydrogen bonds : angle 3.89865 / 2.71 ( 864) Misc. bond : bond 0.00015 / 0.01 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.8267 (tmtt) cc_final: 0.7586 (tptm) REVERT: A 73 ASN cc_start: 0.7245 (t0) cc_final: 0.6667 (t0) REVERT: A 116 GLU cc_start: 0.8698 (mp0) cc_final: 0.8071 (mp0) REVERT: A 123 MET cc_start: 0.4283 (mmt) cc_final: 0.3440 (mtt) REVERT: A 170 GLN cc_start: 0.8857 (tt0) cc_final: 0.8492 (tt0) REVERT: A 186 ASN cc_start: 0.8584 (m-40) cc_final: 0.8140 (m110) REVERT: A 262 PRO cc_start: 0.7665 (Cg_exo) cc_final: 0.7390 (Cg_endo) REVERT: B 62 LYS cc_start: 0.8247 (tmtt) cc_final: 0.7567 (tptm) REVERT: B 73 ASN cc_start: 0.7238 (t0) cc_final: 0.6669 (t0) REVERT: B 116 GLU cc_start: 0.8695 (mp0) cc_final: 0.8066 (mp0) REVERT: B 123 MET cc_start: 0.4286 (mmt) cc_final: 0.3448 (mtt) REVERT: B 150 GLN cc_start: 0.8267 (tp40) cc_final: 0.8031 (tp-100) REVERT: B 186 ASN cc_start: 0.8569 (m-40) cc_final: 0.8145 (m110) REVERT: B 262 PRO cc_start: 0.7666 (Cg_exo) cc_final: 0.7404 (Cg_endo) REVERT: C 62 LYS cc_start: 0.8249 (tmtt) cc_final: 0.7569 (tptm) REVERT: C 73 ASN cc_start: 0.7244 (t0) cc_final: 0.6678 (t0) REVERT: C 116 GLU cc_start: 0.8700 (mp0) cc_final: 0.8068 (mp0) REVERT: C 123 MET cc_start: 0.4335 (mmt) cc_final: 0.3473 (mtt) REVERT: C 150 GLN cc_start: 0.8263 (tp40) cc_final: 0.8028 (tp-100) REVERT: C 186 ASN cc_start: 0.8572 (m-40) cc_final: 0.8142 (m110) REVERT: C 262 PRO cc_start: 0.7664 (Cg_exo) cc_final: 0.7389 (Cg_endo) REVERT: D 62 LYS cc_start: 0.8255 (tmtt) cc_final: 0.7575 (tptm) REVERT: D 73 ASN cc_start: 0.7246 (t0) cc_final: 0.6673 (t0) REVERT: D 94 GLU cc_start: 0.8386 (tt0) cc_final: 0.8117 (tt0) REVERT: D 116 GLU cc_start: 0.8697 (mp0) cc_final: 0.8053 (mp0) REVERT: D 123 MET cc_start: 0.4290 (mmt) cc_final: 0.3439 (mtt) REVERT: D 170 GLN cc_start: 0.8879 (tt0) cc_final: 0.8662 (tt0) REVERT: D 186 ASN cc_start: 0.8580 (m-40) cc_final: 0.8149 (m110) REVERT: D 262 PRO cc_start: 0.7668 (Cg_exo) cc_final: 0.7393 (Cg_endo) outliers start: 39 outliers final: 34 residues processed: 236 average time/residue: 0.0705 time to fit residues: 23.3925 Evaluate side-chains 253 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 254 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: [46, 79, 66, 28, 61, 52, 4, 12, 23, 49, 56] chunk 46 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 HIS B 150 GLN C 74 HIS D 74 HIS ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.176924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.140658 restraints weight = 8745.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.145475 restraints weight = 5224.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.148893 restraints weight = 3836.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.151178 restraints weight = 3120.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.152762 restraints weight = 2707.779| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7336 Z= 0.193 Angle : 0.607 5.824 9884 Z= 0.332 Chirality : 0.040 0.139 1176 Planarity : 0.004 0.047 1248 Dihedral : 6.535 59.018 1042 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 4.87 % Allowed : 31.67 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.29), residues: 912 helix: 1.54 (0.25), residues: 420 sheet: -3.41 (0.33), residues: 168 loop : -1.11 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 308 TYR 0.004 0.001 TYR A 55 PHE 0.006 0.001 PHE A 161 TRP 0.009 0.001 TRP A 304 HIS 0.009 0.002 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 ( 7332) covalent geometry : angle 0.60743 / 0.33 ( 9884) hydrogen bonds : bond 0.05110 / 3.26 ( 312) hydrogen bonds : angle 3.96097 / 2.77 ( 864) Misc. bond : bond 0.00027 / 0.02 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1250.40 seconds wall clock time: 22 minutes 19.80 seconds (1339.80 seconds total)