Starting phenix.real_space_refine on Wed Mar 4 11:53:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k24_22642/03_2026/7k24_22642.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k24_22642/03_2026/7k24_22642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k24_22642/03_2026/7k24_22642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k24_22642/03_2026/7k24_22642.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k24_22642/03_2026/7k24_22642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k24_22642/03_2026/7k24_22642.map" } resolution = 2.9 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 ------------------------------------------------------------------------------- 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= 1.000 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 80 5.16 5 C 8695 2.51 5 N 2300 2.21 5 O 2675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13750 Number of models: 1 Model: "" Number of chains: 1 Chain: "F1" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 30, 'TRANS': 322} Restraints were copied for chains: F2, F3, F4, F5 Time building chain proxies: 2.13, per 1000 atoms: 0.15 Number of scatterers: 13750 At special positions: 0 Unit cell: (140.8, 136.4, 90.2, 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 80 16.00 O 2675 8.00 N 2300 7.00 C 8695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYSF1 19 " - pdb=" SG CYSF2 114 " distance=2.05 Simple disulfide: pdb=" SG CYSF1 114 " - pdb=" SG CYSF5 19 " distance=2.05 Simple disulfide: pdb=" SG CYSF2 19 " - pdb=" SG CYSF3 114 " distance=2.00 Simple disulfide: pdb=" SG CYSF3 19 " - pdb=" SG CYSF4 114 " distance=2.04 Simple disulfide: pdb=" SG CYSF4 19 " - pdb=" SG CYSF5 114 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 632.0 milliseconds 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 25 sheets defined 12.2% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'F1' and resid 33 through 39 Processing helix chain 'F1' and resid 91 through 95 Processing helix chain 'F1' and resid 131 through 137 Processing helix chain 'F1' and resid 192 through 197 removed outlier: 3.527A pdb=" N ILEF1 196 " --> pdb=" O THRF1 192 " (cutoff:3.500A) Processing helix chain 'F1' and resid 202 through 207 Processing helix chain 'F1' and resid 322 through 333 removed outlier: 4.084A pdb=" N SERF1 326 " --> pdb=" O ALAF1 322 " (cutoff:3.500A) Processing helix chain 'F2' and resid 33 through 39 Processing helix chain 'F2' and resid 91 through 95 Processing helix chain 'F2' and resid 131 through 137 Processing helix chain 'F2' and resid 192 through 197 removed outlier: 3.527A pdb=" N ILEF2 196 " --> pdb=" O THRF2 192 " (cutoff:3.500A) Processing helix chain 'F2' and resid 202 through 207 Processing helix chain 'F2' and resid 322 through 333 removed outlier: 4.083A pdb=" N SERF2 326 " --> pdb=" O ALAF2 322 " (cutoff:3.500A) Processing helix chain 'F3' and resid 33 through 39 Processing helix chain 'F3' and resid 91 through 95 Processing helix chain 'F3' and resid 131 through 137 Processing helix chain 'F3' and resid 192 through 197 removed outlier: 3.527A pdb=" N ILEF3 196 " --> pdb=" O THRF3 192 " (cutoff:3.500A) Processing helix chain 'F3' and resid 202 through 207 Processing helix chain 'F3' and resid 322 through 333 removed outlier: 4.084A pdb=" N SERF3 326 " --> pdb=" O ALAF3 322 " (cutoff:3.500A) Processing helix chain 'F4' and resid 33 through 39 Processing helix chain 'F4' and resid 91 through 95 Processing helix chain 'F4' and resid 131 through 137 Processing helix chain 'F4' and resid 192 through 197 removed outlier: 3.527A pdb=" N ILEF4 196 " --> pdb=" O THRF4 192 " (cutoff:3.500A) Processing helix chain 'F4' and resid 202 through 207 Processing helix chain 'F4' and resid 322 through 333 removed outlier: 4.084A pdb=" N SERF4 326 " --> pdb=" O ALAF4 322 " (cutoff:3.500A) Processing helix chain 'F5' and resid 33 through 39 Processing helix chain 'F5' and resid 91 through 95 Processing helix chain 'F5' and resid 131 through 137 Processing helix chain 'F5' and resid 192 through 197 removed outlier: 3.527A pdb=" N ILEF5 196 " --> pdb=" O THRF5 192 " (cutoff:3.500A) Processing helix chain 'F5' and resid 202 through 207 Processing helix chain 'F5' and resid 322 through 333 removed outlier: 4.083A pdb=" N SERF5 326 " --> pdb=" O ALAF5 322 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F1' and resid 47 through 53 removed outlier: 6.499A pdb=" N TYRF1 305 " --> pdb=" O THRF1 127 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THRF1 127 " --> pdb=" O TYRF1 305 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYSF1 307 " --> pdb=" O VALF1 125 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VALF1 125 " --> pdb=" O LYSF1 307 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THRF1 309 " --> pdb=" O VALF1 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F1' and resid 99 through 104 removed outlier: 6.625A pdb=" N ARGF1 300 " --> pdb=" O METF1 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F1' and resid 99 through 104 Processing sheet with id=AA4, first strand: chain 'F1' and resid 144 through 146 removed outlier: 6.496A pdb=" N ILEF1 153 " --> pdb=" O PROF1 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F1' and resid 213 through 215 Processing sheet with id=AA6, first strand: chain 'F1' and resid 252 through 256 Processing sheet with id=AA7, first strand: chain 'F1' and resid 252 through 256 removed outlier: 6.625A pdb=" N ARGF2 300 " --> pdb=" O METF2 286 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F2' and resid 47 through 53 removed outlier: 6.500A pdb=" N TYRF2 305 " --> pdb=" O THRF2 127 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THRF2 127 " --> pdb=" O TYRF2 305 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYSF2 307 " --> pdb=" O VALF2 125 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VALF2 125 " --> pdb=" O LYSF2 307 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THRF2 309 " --> pdb=" O VALF2 123 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F2' and resid 144 through 146 removed outlier: 6.496A pdb=" N ILEF2 153 " --> pdb=" O PROF2 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F2' and resid 213 through 215 Processing sheet with id=AB2, first strand: chain 'F2' and resid 252 through 256 Processing sheet with id=AB3, first strand: chain 'F2' and resid 252 through 256 removed outlier: 6.625A pdb=" N ARGF3 300 " --> pdb=" O METF3 286 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F3' and resid 47 through 53 removed outlier: 6.500A pdb=" N TYRF3 305 " --> pdb=" O THRF3 127 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THRF3 127 " --> pdb=" O TYRF3 305 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYSF3 307 " --> pdb=" O VALF3 125 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VALF3 125 " --> pdb=" O LYSF3 307 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THRF3 309 " --> pdb=" O VALF3 123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F3' and resid 144 through 146 removed outlier: 6.495A pdb=" N ILEF3 153 " --> pdb=" O PROF3 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F3' and resid 213 through 215 Processing sheet with id=AB7, first strand: chain 'F3' and resid 252 through 256 Processing sheet with id=AB8, first strand: chain 'F3' and resid 252 through 256 removed outlier: 6.625A pdb=" N ARGF4 300 " --> pdb=" O METF4 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F4' and resid 47 through 53 removed outlier: 6.499A pdb=" N TYRF4 305 " --> pdb=" O THRF4 127 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THRF4 127 " --> pdb=" O TYRF4 305 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYSF4 307 " --> pdb=" O VALF4 125 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VALF4 125 " --> pdb=" O LYSF4 307 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THRF4 309 " --> pdb=" O VALF4 123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F4' and resid 144 through 146 removed outlier: 6.495A pdb=" N ILEF4 153 " --> pdb=" O PROF4 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F4' and resid 213 through 215 Processing sheet with id=AC3, first strand: chain 'F4' and resid 252 through 256 Processing sheet with id=AC4, first strand: chain 'F4' and resid 252 through 256 removed outlier: 6.626A pdb=" N ARGF5 300 " --> pdb=" O METF5 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F5' and resid 47 through 53 removed outlier: 6.499A pdb=" N TYRF5 305 " --> pdb=" O THRF5 127 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THRF5 127 " --> pdb=" O TYRF5 305 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYSF5 307 " --> pdb=" O VALF5 125 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VALF5 125 " --> pdb=" O LYSF5 307 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THRF5 309 " --> pdb=" O VALF5 123 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F5' and resid 144 through 146 removed outlier: 6.495A pdb=" N ILEF5 153 " --> pdb=" O PROF5 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F5' and resid 213 through 215 441 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4515 1.34 - 1.46: 2650 1.46 - 1.58: 6785 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 14090 Sorted by residual: bond pdb=" CA GLNF4 71 " pdb=" C GLNF4 71 " ideal model delta sigma weight residual 1.532 1.518 0.014 9.60e-03 1.09e+04 2.10e+00 bond pdb=" CA GLNF2 71 " pdb=" C GLNF2 71 " ideal model delta sigma weight residual 1.532 1.519 0.014 9.60e-03 1.09e+04 2.05e+00 bond pdb=" CA GLNF1 71 " pdb=" C GLNF1 71 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.94e+00 bond pdb=" CA GLNF5 71 " pdb=" C GLNF5 71 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.84e+00 bond pdb=" CA GLNF3 71 " pdb=" C GLNF3 71 " ideal model delta sigma weight residual 1.532 1.520 0.013 9.60e-03 1.09e+04 1.78e+00 ... (remaining 14085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 17768 1.35 - 2.70: 1205 2.70 - 4.05: 187 4.05 - 5.40: 60 5.40 - 6.75: 10 Bond angle restraints: 19230 Sorted by residual: angle pdb=" N GLYF5 275 " pdb=" CA GLYF5 275 " pdb=" C GLYF5 275 " ideal model delta sigma weight residual 113.18 106.43 6.75 2.37e+00 1.78e-01 8.12e+00 angle pdb=" N GLYF4 275 " pdb=" CA GLYF4 275 " pdb=" C GLYF4 275 " ideal model delta sigma weight residual 113.18 106.44 6.74 2.37e+00 1.78e-01 8.10e+00 angle pdb=" N GLYF1 275 " pdb=" CA GLYF1 275 " pdb=" C GLYF1 275 " ideal model delta sigma weight residual 113.18 106.45 6.73 2.37e+00 1.78e-01 8.07e+00 angle pdb=" N GLYF3 275 " pdb=" CA GLYF3 275 " pdb=" C GLYF3 275 " ideal model delta sigma weight residual 113.18 106.45 6.73 2.37e+00 1.78e-01 8.06e+00 angle pdb=" N GLYF2 275 " pdb=" CA GLYF2 275 " pdb=" C GLYF2 275 " ideal model delta sigma weight residual 113.18 106.46 6.72 2.37e+00 1.78e-01 8.04e+00 ... (remaining 19225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 7219 16.57 - 33.15: 822 33.15 - 49.72: 299 49.72 - 66.30: 155 66.30 - 82.87: 25 Dihedral angle restraints: 8520 sinusoidal: 3475 harmonic: 5045 Sorted by residual: dihedral pdb=" CA METF2 321 " pdb=" C METF2 321 " pdb=" N ALAF2 322 " pdb=" CA ALAF2 322 " ideal model delta harmonic sigma weight residual 180.00 153.51 26.49 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA METF3 321 " pdb=" C METF3 321 " pdb=" N ALAF3 322 " pdb=" CA ALAF3 322 " ideal model delta harmonic sigma weight residual 180.00 153.53 26.47 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA METF1 321 " pdb=" C METF1 321 " pdb=" N ALAF1 322 " pdb=" CA ALAF1 322 " ideal model delta harmonic sigma weight residual 180.00 153.55 26.45 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 8517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1017 0.028 - 0.056: 735 0.056 - 0.084: 189 0.084 - 0.112: 180 0.112 - 0.140: 34 Chirality restraints: 2155 Sorted by residual: chirality pdb=" CA THRF4 62 " pdb=" N THRF4 62 " pdb=" C THRF4 62 " pdb=" CB THRF4 62 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA THRF5 62 " pdb=" N THRF5 62 " pdb=" C THRF5 62 " pdb=" CB THRF5 62 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA THRF2 62 " pdb=" N THRF2 62 " pdb=" C THRF2 62 " pdb=" CB THRF2 62 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 2152 not shown) Planarity restraints: 2510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SERF3 89 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PROF3 90 " -0.100 5.00e-02 4.00e+02 pdb=" CA PROF3 90 " 0.030 5.00e-02 4.00e+02 pdb=" CD PROF3 90 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SERF5 89 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PROF5 90 " 0.100 5.00e-02 4.00e+02 pdb=" CA PROF5 90 " -0.030 5.00e-02 4.00e+02 pdb=" CD PROF5 90 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SERF4 89 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PROF4 90 " 0.099 5.00e-02 4.00e+02 pdb=" CA PROF4 90 " -0.030 5.00e-02 4.00e+02 pdb=" CD PROF4 90 " -0.032 5.00e-02 4.00e+02 ... (remaining 2507 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2782 2.77 - 3.30: 11589 3.30 - 3.84: 22479 3.84 - 4.37: 27773 4.37 - 4.90: 46427 Nonbonded interactions: 111050 Sorted by model distance: nonbonded pdb=" O LYSF5 143 " pdb=" OG1 THRF5 155 " model vdw 2.240 3.040 nonbonded pdb=" O LYSF2 143 " pdb=" OG1 THRF2 155 " model vdw 2.241 3.040 nonbonded pdb=" O LYSF4 143 " pdb=" OG1 THRF4 155 " model vdw 2.241 3.040 nonbonded pdb=" O LYSF3 143 " pdb=" OG1 THRF3 155 " model vdw 2.241 3.040 nonbonded pdb=" O LYSF1 143 " pdb=" OG1 THRF1 155 " model vdw 2.241 3.040 ... (remaining 111045 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: 0.04 Found NCS groups: ncs_group { reference = chain 'F1' selection = chain 'F2' selection = chain 'F3' selection = chain 'F4' selection = chain 'F5' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.990 Find NCS groups from input model: 0.120 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:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14095 Z= 0.228 Angle : 0.774 6.754 19240 Z= 0.437 Chirality : 0.046 0.140 2155 Planarity : 0.006 0.058 2510 Dihedral : 18.357 82.870 5285 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.64 % Favored : 91.79 % Rotamer: Outliers : 12.54 % Allowed : 18.01 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.66 (0.17), residues: 1755 helix: -4.73 (0.12), residues: 120 sheet: -0.84 (0.23), residues: 455 loop : -3.05 (0.15), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGF3 289 TYR 0.011 0.001 TYRF5 239 PHE 0.015 0.002 PHEF3 306 TRP 0.012 0.002 TRPF5 299 HIS 0.003 0.001 HISF4 139 Details of bonding type rmsd covalent geometry : bond 0.00502 (14090) covalent geometry : angle 0.77346 (19230) SS BOND : bond 0.01930 ( 5) SS BOND : angle 1.27471 ( 10) hydrogen bonds : bond 0.16845 ( 355) hydrogen bonds : angle 8.48060 ( 1008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 314 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F1 79 ILE cc_start: 0.6502 (OUTLIER) cc_final: 0.6230 (mt) REVERT: F1 91 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6501 (tp30) REVERT: F1 93 ASN cc_start: 0.8085 (p0) cc_final: 0.7811 (p0) REVERT: F1 158 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7855 (mt-10) REVERT: F1 188 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: F1 204 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8013 (mttt) REVERT: F1 215 LYS cc_start: 0.8294 (mttm) cc_final: 0.7949 (mtpt) REVERT: F1 254 GLN cc_start: 0.8330 (mt0) cc_final: 0.8125 (mp10) REVERT: F1 292 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7617 (mtt180) REVERT: F1 316 LYS cc_start: 0.6247 (mttp) cc_final: 0.5148 (mmtm) REVERT: F2 91 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6449 (tp30) REVERT: F2 111 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7082 (m-30) REVERT: F2 112 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8299 (mm) REVERT: F2 158 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7922 (mt-10) REVERT: F2 196 ILE cc_start: 0.8949 (mm) cc_final: 0.8712 (mp) REVERT: F2 215 LYS cc_start: 0.8268 (mttm) cc_final: 0.8040 (mttp) REVERT: F2 292 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7766 (mtt180) REVERT: F2 316 LYS cc_start: 0.6095 (mttp) cc_final: 0.4970 (mmtm) REVERT: F3 21 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7522 (ttm170) REVERT: F3 47 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8648 (m) REVERT: F3 80 ASN cc_start: 0.7445 (OUTLIER) cc_final: 0.7084 (m-40) REVERT: F3 111 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7010 (m-30) REVERT: F3 117 LEU cc_start: 0.8336 (tp) cc_final: 0.8126 (tp) REVERT: F3 151 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8092 (mttm) REVERT: F3 215 LYS cc_start: 0.8195 (mttm) cc_final: 0.7890 (mtpt) REVERT: F3 221 MET cc_start: 0.8389 (mmm) cc_final: 0.8179 (mmm) REVERT: F3 254 GLN cc_start: 0.8274 (mt0) cc_final: 0.8035 (mp10) REVERT: F3 257 ASN cc_start: 0.7807 (t0) cc_final: 0.7558 (t0) REVERT: F3 266 GLU cc_start: 0.7967 (mp0) cc_final: 0.7422 (tt0) REVERT: F3 292 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7871 (mtt180) REVERT: F3 316 LYS cc_start: 0.5997 (mttp) cc_final: 0.4915 (mmtm) REVERT: F3 341 MET cc_start: 0.9043 (mmt) cc_final: 0.8814 (mmt) REVERT: F4 91 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6504 (tp30) REVERT: F4 111 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.6794 (m-30) REVERT: F4 143 LYS cc_start: 0.8326 (tttt) cc_final: 0.8043 (tttm) REVERT: F4 158 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7898 (mt-10) REVERT: F4 187 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7867 (mt-10) REVERT: F4 316 LYS cc_start: 0.6200 (mttp) cc_final: 0.5151 (mmtm) REVERT: F4 341 MET cc_start: 0.8946 (mmt) cc_final: 0.7919 (mmt) REVERT: F5 91 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6435 (tp30) REVERT: F5 111 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7130 (m-30) REVERT: F5 112 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8190 (mm) REVERT: F5 143 LYS cc_start: 0.8232 (tttt) cc_final: 0.7969 (ttmt) REVERT: F5 215 LYS cc_start: 0.8359 (mttm) cc_final: 0.7941 (mttt) REVERT: F5 257 ASN cc_start: 0.7987 (t0) cc_final: 0.7772 (t0) REVERT: F5 292 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7868 (mtt180) REVERT: F5 316 LYS cc_start: 0.6225 (mttp) cc_final: 0.5114 (tptt) outliers start: 195 outliers final: 35 residues processed: 435 average time/residue: 0.5837 time to fit residues: 277.2306 Evaluate side-chains 310 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 255 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 36 VAL Chi-restraints excluded: chain F1 residue 71 GLN Chi-restraints excluded: chain F1 residue 79 ILE Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 91 GLU Chi-restraints excluded: chain F1 residue 112 LEU Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 188 GLU Chi-restraints excluded: chain F1 residue 217 ASP Chi-restraints excluded: chain F1 residue 252 VAL Chi-restraints excluded: chain F1 residue 292 ARG Chi-restraints excluded: chain F1 residue 367 THR Chi-restraints excluded: chain F1 residue 370 VAL Chi-restraints excluded: chain F2 residue 36 VAL Chi-restraints excluded: chain F2 residue 86 THR Chi-restraints excluded: chain F2 residue 91 GLU Chi-restraints excluded: chain F2 residue 111 ASP Chi-restraints excluded: chain F2 residue 112 LEU Chi-restraints excluded: chain F2 residue 154 SER Chi-restraints excluded: chain F2 residue 292 ARG Chi-restraints excluded: chain F2 residue 367 THR Chi-restraints excluded: chain F3 residue 21 ARG Chi-restraints excluded: chain F3 residue 36 VAL Chi-restraints excluded: chain F3 residue 44 ASP Chi-restraints excluded: chain F3 residue 47 THR Chi-restraints excluded: chain F3 residue 68 GLU Chi-restraints excluded: chain F3 residue 71 GLN Chi-restraints excluded: chain F3 residue 80 ASN Chi-restraints excluded: chain F3 residue 86 THR Chi-restraints excluded: chain F3 residue 110 GLU Chi-restraints excluded: chain F3 residue 111 ASP Chi-restraints excluded: chain F3 residue 151 LYS Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 217 ASP Chi-restraints excluded: chain F3 residue 292 ARG Chi-restraints excluded: chain F3 residue 367 THR Chi-restraints excluded: chain F3 residue 370 VAL Chi-restraints excluded: chain F4 residue 36 VAL Chi-restraints excluded: chain F4 residue 71 GLN Chi-restraints excluded: chain F4 residue 86 THR Chi-restraints excluded: chain F4 residue 91 GLU Chi-restraints excluded: chain F4 residue 111 ASP Chi-restraints excluded: chain F4 residue 112 LEU Chi-restraints excluded: chain F4 residue 154 SER Chi-restraints excluded: chain F4 residue 367 THR Chi-restraints excluded: chain F4 residue 370 VAL Chi-restraints excluded: chain F5 residue 71 GLN Chi-restraints excluded: chain F5 residue 86 THR Chi-restraints excluded: chain F5 residue 91 GLU Chi-restraints excluded: chain F5 residue 111 ASP Chi-restraints excluded: chain F5 residue 112 LEU Chi-restraints excluded: chain F5 residue 154 SER Chi-restraints excluded: chain F5 residue 292 ARG Chi-restraints excluded: chain F5 residue 367 THR Chi-restraints excluded: chain F5 residue 370 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1 54 ASN ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1 118 GLN F1 142 ASN F1 149 ASN F1 163 HIS F1 254 GLN F1 339 GLN F1 347 GLN F2 54 ASN ** F2 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 118 GLN F2 142 ASN F2 163 HIS F2 206 GLN F2 257 ASN F2 339 GLN F2 347 GLN F3 54 ASN ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 118 GLN F3 142 ASN F3 163 HIS F3 206 GLN F3 254 GLN F3 257 ASN F3 339 GLN F3 347 GLN F4 54 ASN ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 118 GLN F4 142 ASN F4 163 HIS F4 206 GLN F4 257 ASN F4 339 GLN F4 347 GLN F5 54 ASN ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 80 ASN F5 92 ASN ** F5 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 118 GLN F5 142 ASN F5 163 HIS F5 206 GLN F5 257 ASN F5 339 GLN F5 347 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.145411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.113180 restraints weight = 13684.570| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.72 r_work: 0.2864 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14095 Z= 0.122 Angle : 0.611 7.259 19240 Z= 0.310 Chirality : 0.043 0.131 2155 Planarity : 0.005 0.040 2510 Dihedral : 10.286 89.405 1998 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 7.65 % Allowed : 21.67 % Favored : 70.68 % 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: -2.55 (0.19), residues: 1755 helix: -2.93 (0.43), residues: 120 sheet: -0.16 (0.24), residues: 450 loop : -2.35 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARGF5 289 TYR 0.011 0.001 TYRF1 239 PHE 0.011 0.002 PHEF3 165 TRP 0.014 0.002 TRPF1 299 HIS 0.003 0.001 HISF4 297 Details of bonding type rmsd covalent geometry : bond 0.00291 (14090) covalent geometry : angle 0.61140 (19230) SS BOND : bond 0.00034 ( 5) SS BOND : angle 0.28231 ( 10) hydrogen bonds : bond 0.02987 ( 355) hydrogen bonds : angle 5.12610 ( 1008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 269 time to evaluate : 0.542 Fit side-chains REVERT: F1 158 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8469 (mt-10) REVERT: F1 187 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7975 (mm-30) REVERT: F1 188 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8036 (mp0) REVERT: F1 199 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7848 (mptt) REVERT: F1 215 LYS cc_start: 0.8597 (mttm) cc_final: 0.8247 (mtpt) REVERT: F1 316 LYS cc_start: 0.6572 (mttp) cc_final: 0.4944 (mmtm) REVERT: F2 34 MET cc_start: 0.8296 (mmt) cc_final: 0.8084 (tpt) REVERT: F2 110 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6675 (pt0) REVERT: F2 111 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: F2 158 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8578 (mt-10) REVERT: F2 215 LYS cc_start: 0.8546 (mttm) cc_final: 0.8303 (mttt) REVERT: F2 316 LYS cc_start: 0.6414 (mttp) cc_final: 0.4621 (tppt) REVERT: F2 363 ASP cc_start: 0.7327 (t70) cc_final: 0.6945 (t0) REVERT: F3 21 ARG cc_start: 0.8315 (mmp80) cc_final: 0.7650 (mtt90) REVERT: F3 68 GLU cc_start: 0.4916 (OUTLIER) cc_final: 0.4675 (pm20) REVERT: F3 80 ASN cc_start: 0.7979 (OUTLIER) cc_final: 0.7752 (p0) REVERT: F3 111 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7158 (m-30) REVERT: F3 158 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8519 (mt-10) REVERT: F3 254 GLN cc_start: 0.9024 (mt0) cc_final: 0.8630 (mp10) REVERT: F3 316 LYS cc_start: 0.6128 (mttp) cc_final: 0.4506 (mmtm) REVERT: F3 321 MET cc_start: 0.6023 (OUTLIER) cc_final: 0.5445 (mtm) REVERT: F3 337 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.6390 (mt0) REVERT: F4 57 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7588 (mmm) REVERT: F4 88 ASP cc_start: 0.7724 (t0) cc_final: 0.7498 (t0) REVERT: F4 91 GLU cc_start: 0.7301 (tp30) cc_final: 0.7005 (tp30) REVERT: F4 110 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6286 (pp20) REVERT: F4 111 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.6906 (m-30) REVERT: F4 112 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8167 (mt) REVERT: F4 158 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8703 (mt-10) REVERT: F4 184 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8191 (mtmt) REVERT: F4 187 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8107 (mm-30) REVERT: F4 316 LYS cc_start: 0.6314 (mttp) cc_final: 0.4701 (mmtm) REVERT: F4 337 GLN cc_start: 0.6836 (OUTLIER) cc_final: 0.6620 (mt0) REVERT: F4 341 MET cc_start: 0.9125 (mmt) cc_final: 0.7988 (mmt) REVERT: F4 363 ASP cc_start: 0.7490 (t70) cc_final: 0.7217 (t0) REVERT: F5 110 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6259 (pt0) REVERT: F5 111 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7250 (m-30) REVERT: F5 146 ASP cc_start: 0.6623 (OUTLIER) cc_final: 0.6420 (m-30) REVERT: F5 158 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8601 (mt-10) REVERT: F5 187 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7792 (mm-30) REVERT: F5 208 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8194 (tt) REVERT: F5 215 LYS cc_start: 0.8530 (mttm) cc_final: 0.8159 (mttt) REVERT: F5 254 GLN cc_start: 0.8998 (mt0) cc_final: 0.8662 (mp10) REVERT: F5 316 LYS cc_start: 0.6532 (mttp) cc_final: 0.4826 (tptt) outliers start: 119 outliers final: 33 residues processed: 343 average time/residue: 0.5450 time to fit residues: 205.4514 Evaluate side-chains 290 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 237 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 67 THR Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 187 GLU Chi-restraints excluded: chain F1 residue 199 LYS Chi-restraints excluded: chain F1 residue 207 VAL Chi-restraints excluded: chain F1 residue 217 ASP Chi-restraints excluded: chain F1 residue 253 LEU Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F2 residue 57 MET Chi-restraints excluded: chain F2 residue 65 SER Chi-restraints excluded: chain F2 residue 67 THR Chi-restraints excluded: chain F2 residue 110 GLU Chi-restraints excluded: chain F2 residue 111 ASP Chi-restraints excluded: chain F2 residue 207 VAL Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 319 TYR Chi-restraints excluded: chain F3 residue 67 THR Chi-restraints excluded: chain F3 residue 68 GLU Chi-restraints excluded: chain F3 residue 71 GLN Chi-restraints excluded: chain F3 residue 80 ASN Chi-restraints excluded: chain F3 residue 111 ASP Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 199 LYS Chi-restraints excluded: chain F3 residue 206 GLN Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 208 LEU Chi-restraints excluded: chain F3 residue 282 CYS Chi-restraints excluded: chain F3 residue 321 MET Chi-restraints excluded: chain F3 residue 337 GLN Chi-restraints excluded: chain F4 residue 57 MET Chi-restraints excluded: chain F4 residue 67 THR Chi-restraints excluded: chain F4 residue 83 THR Chi-restraints excluded: chain F4 residue 110 GLU Chi-restraints excluded: chain F4 residue 111 ASP Chi-restraints excluded: chain F4 residue 112 LEU Chi-restraints excluded: chain F4 residue 184 LYS Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 208 LEU Chi-restraints excluded: chain F4 residue 260 THR Chi-restraints excluded: chain F4 residue 282 CYS Chi-restraints excluded: chain F4 residue 319 TYR Chi-restraints excluded: chain F4 residue 323 SER Chi-restraints excluded: chain F4 residue 337 GLN Chi-restraints excluded: chain F5 residue 67 THR Chi-restraints excluded: chain F5 residue 83 THR Chi-restraints excluded: chain F5 residue 110 GLU Chi-restraints excluded: chain F5 residue 111 ASP Chi-restraints excluded: chain F5 residue 146 ASP Chi-restraints excluded: chain F5 residue 187 GLU Chi-restraints excluded: chain F5 residue 199 LYS Chi-restraints excluded: chain F5 residue 208 LEU Chi-restraints excluded: chain F5 residue 281 SER Chi-restraints excluded: chain F5 residue 282 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 108 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 92 ASN ** F3 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 92 ASN ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.147046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.117758 restraints weight = 13924.091| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.66 r_work: 0.2957 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14095 Z= 0.114 Angle : 0.581 6.181 19240 Z= 0.292 Chirality : 0.043 0.151 2155 Planarity : 0.005 0.034 2510 Dihedral : 6.692 84.665 1912 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 6.56 % Allowed : 23.47 % Favored : 69.97 % 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: -1.95 (0.19), residues: 1755 helix: -1.58 (0.52), residues: 85 sheet: 0.05 (0.24), residues: 450 loop : -1.95 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGF2 313 TYR 0.011 0.001 TYRF4 239 PHE 0.010 0.002 PHEF1 255 TRP 0.014 0.001 TRPF1 299 HIS 0.003 0.001 HISF2 297 Details of bonding type rmsd covalent geometry : bond 0.00281 (14090) covalent geometry : angle 0.58125 (19230) SS BOND : bond 0.00034 ( 5) SS BOND : angle 0.22847 ( 10) hydrogen bonds : bond 0.02723 ( 355) hydrogen bonds : angle 4.81935 ( 1008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 249 time to evaluate : 0.466 Fit side-chains REVERT: F1 21 ARG cc_start: 0.8151 (mmt-90) cc_final: 0.7661 (mtt180) REVERT: F1 57 MET cc_start: 0.7401 (mtp) cc_final: 0.7101 (mtp) REVERT: F1 119 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8796 (ptm) REVERT: F1 158 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8378 (mt-10) REVERT: F1 187 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7977 (mm-30) REVERT: F1 188 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7908 (mp0) REVERT: F1 199 LYS cc_start: 0.8511 (mtmt) cc_final: 0.7915 (mptt) REVERT: F1 215 LYS cc_start: 0.8540 (mttm) cc_final: 0.8178 (mtpt) REVERT: F1 254 GLN cc_start: 0.9009 (mt0) cc_final: 0.8654 (mp10) REVERT: F1 292 ARG cc_start: 0.8001 (ttt180) cc_final: 0.7703 (mtt-85) REVERT: F1 316 LYS cc_start: 0.6484 (mttp) cc_final: 0.4864 (mmtm) REVERT: F1 363 ASP cc_start: 0.7778 (t0) cc_final: 0.7477 (t0) REVERT: F2 111 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7076 (m-30) REVERT: F2 119 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8965 (ptm) REVERT: F2 158 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8476 (mt-10) REVERT: F2 215 LYS cc_start: 0.8552 (mttm) cc_final: 0.8279 (mtpt) REVERT: F2 316 LYS cc_start: 0.6254 (mttp) cc_final: 0.4576 (tppt) REVERT: F2 363 ASP cc_start: 0.7429 (t70) cc_final: 0.7007 (t0) REVERT: F3 21 ARG cc_start: 0.8238 (mmp80) cc_final: 0.7635 (mtt-85) REVERT: F3 111 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7018 (m-30) REVERT: F3 119 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8677 (ptm) REVERT: F3 158 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8470 (mt-10) REVERT: F3 254 GLN cc_start: 0.8902 (mt0) cc_final: 0.8497 (mp10) REVERT: F3 286 MET cc_start: 0.8912 (mmm) cc_final: 0.8623 (mmm) REVERT: F3 316 LYS cc_start: 0.6075 (mttp) cc_final: 0.4455 (mmtm) REVERT: F3 337 GLN cc_start: 0.6789 (OUTLIER) cc_final: 0.6361 (mt0) REVERT: F3 363 ASP cc_start: 0.7936 (t0) cc_final: 0.7687 (t0) REVERT: F4 50 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7792 (mt-10) REVERT: F4 57 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7368 (mmm) REVERT: F4 91 GLU cc_start: 0.7147 (tp30) cc_final: 0.6856 (tp30) REVERT: F4 111 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.6739 (m-30) REVERT: F4 158 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8607 (mt-10) REVERT: F4 184 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8196 (mtmt) REVERT: F4 316 LYS cc_start: 0.6194 (mttp) cc_final: 0.4621 (mmtm) REVERT: F4 332 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6776 (tmt) REVERT: F4 337 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.6618 (mt0) REVERT: F4 363 ASP cc_start: 0.7503 (t70) cc_final: 0.7242 (t0) REVERT: F5 57 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7048 (ttm) REVERT: F5 110 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.6046 (pt0) REVERT: F5 111 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7205 (m-30) REVERT: F5 119 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8809 (ptm) REVERT: F5 158 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8501 (mt-10) REVERT: F5 187 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: F5 208 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8181 (tt) REVERT: F5 215 LYS cc_start: 0.8551 (mttm) cc_final: 0.8341 (mttt) REVERT: F5 254 GLN cc_start: 0.8833 (mt0) cc_final: 0.8547 (mp10) REVERT: F5 316 LYS cc_start: 0.6382 (mttp) cc_final: 0.4713 (tptt) outliers start: 102 outliers final: 36 residues processed: 310 average time/residue: 0.5941 time to fit residues: 200.9193 Evaluate side-chains 289 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 235 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 107 MET Chi-restraints excluded: chain F1 residue 119 MET Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 252 VAL Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 319 TYR Chi-restraints excluded: chain F1 residue 357 THR Chi-restraints excluded: chain F2 residue 86 THR Chi-restraints excluded: chain F2 residue 111 ASP Chi-restraints excluded: chain F2 residue 119 MET Chi-restraints excluded: chain F2 residue 199 LYS Chi-restraints excluded: chain F2 residue 253 LEU Chi-restraints excluded: chain F2 residue 281 SER Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 357 THR Chi-restraints excluded: chain F3 residue 34 MET Chi-restraints excluded: chain F3 residue 67 THR Chi-restraints excluded: chain F3 residue 111 ASP Chi-restraints excluded: chain F3 residue 119 MET Chi-restraints excluded: chain F3 residue 146 ASP Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 281 SER Chi-restraints excluded: chain F3 residue 282 CYS Chi-restraints excluded: chain F3 residue 319 TYR Chi-restraints excluded: chain F3 residue 337 GLN Chi-restraints excluded: chain F4 residue 50 GLU Chi-restraints excluded: chain F4 residue 57 MET Chi-restraints excluded: chain F4 residue 111 ASP Chi-restraints excluded: chain F4 residue 146 ASP Chi-restraints excluded: chain F4 residue 154 SER Chi-restraints excluded: chain F4 residue 184 LYS Chi-restraints excluded: chain F4 residue 190 VAL Chi-restraints excluded: chain F4 residue 208 LEU Chi-restraints excluded: chain F4 residue 253 LEU Chi-restraints excluded: chain F4 residue 260 THR Chi-restraints excluded: chain F4 residue 281 SER Chi-restraints excluded: chain F4 residue 319 TYR Chi-restraints excluded: chain F4 residue 321 MET Chi-restraints excluded: chain F4 residue 332 MET Chi-restraints excluded: chain F4 residue 337 GLN Chi-restraints excluded: chain F5 residue 57 MET Chi-restraints excluded: chain F5 residue 67 THR Chi-restraints excluded: chain F5 residue 83 THR Chi-restraints excluded: chain F5 residue 110 GLU Chi-restraints excluded: chain F5 residue 111 ASP Chi-restraints excluded: chain F5 residue 119 MET Chi-restraints excluded: chain F5 residue 187 GLU Chi-restraints excluded: chain F5 residue 208 LEU Chi-restraints excluded: chain F5 residue 281 SER Chi-restraints excluded: chain F5 residue 282 CYS Chi-restraints excluded: chain F5 residue 310 LEU Chi-restraints excluded: chain F5 residue 319 TYR Chi-restraints excluded: chain F5 residue 357 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 20 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 36 optimal weight: 0.3980 chunk 21 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 92 ASN ** F3 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.144604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.115438 restraints weight = 13858.725| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.62 r_work: 0.2937 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14095 Z= 0.134 Angle : 0.594 5.930 19240 Z= 0.298 Chirality : 0.043 0.141 2155 Planarity : 0.005 0.031 2510 Dihedral : 5.848 55.370 1900 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 6.43 % Allowed : 23.41 % Favored : 70.16 % 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: -1.69 (0.19), residues: 1755 helix: -0.81 (0.52), residues: 85 sheet: 0.26 (0.25), residues: 450 loop : -1.82 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGF2 313 TYR 0.012 0.001 TYRF4 239 PHE 0.011 0.002 PHEF1 255 TRP 0.013 0.002 TRPF3 299 HIS 0.003 0.001 HISF3 298 Details of bonding type rmsd covalent geometry : bond 0.00329 (14090) covalent geometry : angle 0.59389 (19230) SS BOND : bond 0.00055 ( 5) SS BOND : angle 0.27403 ( 10) hydrogen bonds : bond 0.02752 ( 355) hydrogen bonds : angle 4.79072 ( 1008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 243 time to evaluate : 0.530 Fit side-chains REVERT: F1 21 ARG cc_start: 0.8147 (mmt-90) cc_final: 0.7643 (mtt180) REVERT: F1 57 MET cc_start: 0.7293 (mtp) cc_final: 0.7030 (mtp) REVERT: F1 85 ASP cc_start: 0.8485 (t70) cc_final: 0.8127 (t0) REVERT: F1 88 ASP cc_start: 0.7714 (t0) cc_final: 0.7494 (t0) REVERT: F1 158 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8381 (mt-10) REVERT: F1 187 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8003 (mm-30) REVERT: F1 188 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7844 (mp0) REVERT: F1 199 LYS cc_start: 0.8520 (mtmt) cc_final: 0.7916 (mptt) REVERT: F1 215 LYS cc_start: 0.8645 (mttm) cc_final: 0.8355 (mttp) REVERT: F1 292 ARG cc_start: 0.7969 (ttt180) cc_final: 0.7663 (mtt-85) REVERT: F1 316 LYS cc_start: 0.6560 (mttp) cc_final: 0.4950 (mmtm) REVERT: F1 321 MET cc_start: 0.5969 (mmt) cc_final: 0.5642 (mmm) REVERT: F1 332 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6514 (tmt) REVERT: F2 57 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.6814 (ttm) REVERT: F2 111 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.6859 (m-30) REVERT: F2 112 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8082 (mp) REVERT: F2 158 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8431 (mt-10) REVERT: F2 215 LYS cc_start: 0.8480 (mttm) cc_final: 0.8217 (mttt) REVERT: F2 316 LYS cc_start: 0.6333 (mttp) cc_final: 0.4607 (tppt) REVERT: F2 363 ASP cc_start: 0.7172 (t70) cc_final: 0.6869 (t0) REVERT: F3 21 ARG cc_start: 0.8172 (mmp80) cc_final: 0.7591 (mtt-85) REVERT: F3 111 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.6924 (m-30) REVERT: F3 119 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8685 (ptm) REVERT: F3 254 GLN cc_start: 0.8927 (mt0) cc_final: 0.8513 (mp10) REVERT: F3 316 LYS cc_start: 0.6126 (mttp) cc_final: 0.4473 (mmtm) REVERT: F3 337 GLN cc_start: 0.6751 (OUTLIER) cc_final: 0.6327 (mt0) REVERT: F3 363 ASP cc_start: 0.7853 (t0) cc_final: 0.7639 (t0) REVERT: F4 57 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7295 (mmm) REVERT: F4 91 GLU cc_start: 0.7226 (tp30) cc_final: 0.6910 (tp30) REVERT: F4 111 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.6579 (m-30) REVERT: F4 112 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7868 (mt) REVERT: F4 158 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8596 (mt-10) REVERT: F4 316 LYS cc_start: 0.6233 (mttp) cc_final: 0.4651 (mmtm) REVERT: F4 321 MET cc_start: 0.5471 (OUTLIER) cc_final: 0.4838 (mtm) REVERT: F4 332 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6469 (tmm) REVERT: F4 337 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.6664 (mt0) REVERT: F4 341 MET cc_start: 0.9145 (mmt) cc_final: 0.8103 (mmt) REVERT: F4 363 ASP cc_start: 0.7548 (t70) cc_final: 0.7308 (t0) REVERT: F5 57 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.6868 (ttm) REVERT: F5 85 ASP cc_start: 0.8578 (t70) cc_final: 0.8235 (t0) REVERT: F5 91 GLU cc_start: 0.7175 (tp30) cc_final: 0.6874 (tp30) REVERT: F5 110 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.6117 (pt0) REVERT: F5 158 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8564 (mt-10) REVERT: F5 187 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: F5 215 LYS cc_start: 0.8554 (mttm) cc_final: 0.8332 (mttt) REVERT: F5 316 LYS cc_start: 0.6452 (mttp) cc_final: 0.4780 (tptt) outliers start: 100 outliers final: 50 residues processed: 298 average time/residue: 0.5759 time to fit residues: 187.7808 Evaluate side-chains 300 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 233 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 67 THR Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 137 ASP Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 187 GLU Chi-restraints excluded: chain F1 residue 207 VAL Chi-restraints excluded: chain F1 residue 252 VAL Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 332 MET Chi-restraints excluded: chain F1 residue 357 THR Chi-restraints excluded: chain F2 residue 57 MET Chi-restraints excluded: chain F2 residue 65 SER Chi-restraints excluded: chain F2 residue 67 THR Chi-restraints excluded: chain F2 residue 86 THR Chi-restraints excluded: chain F2 residue 111 ASP Chi-restraints excluded: chain F2 residue 112 LEU Chi-restraints excluded: chain F2 residue 146 ASP Chi-restraints excluded: chain F2 residue 154 SER Chi-restraints excluded: chain F2 residue 253 LEU Chi-restraints excluded: chain F2 residue 281 SER Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 296 VAL Chi-restraints excluded: chain F2 residue 319 TYR Chi-restraints excluded: chain F2 residue 357 THR Chi-restraints excluded: chain F3 residue 36 VAL Chi-restraints excluded: chain F3 residue 67 THR Chi-restraints excluded: chain F3 residue 83 THR Chi-restraints excluded: chain F3 residue 86 THR Chi-restraints excluded: chain F3 residue 111 ASP Chi-restraints excluded: chain F3 residue 119 MET Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 208 LEU Chi-restraints excluded: chain F3 residue 259 LEU Chi-restraints excluded: chain F3 residue 281 SER Chi-restraints excluded: chain F3 residue 282 CYS Chi-restraints excluded: chain F3 residue 337 GLN Chi-restraints excluded: chain F4 residue 57 MET Chi-restraints excluded: chain F4 residue 65 SER Chi-restraints excluded: chain F4 residue 67 THR Chi-restraints excluded: chain F4 residue 86 THR Chi-restraints excluded: chain F4 residue 111 ASP Chi-restraints excluded: chain F4 residue 112 LEU Chi-restraints excluded: chain F4 residue 147 THR Chi-restraints excluded: chain F4 residue 154 SER Chi-restraints excluded: chain F4 residue 190 VAL Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 208 LEU Chi-restraints excluded: chain F4 residue 211 ILE Chi-restraints excluded: chain F4 residue 253 LEU Chi-restraints excluded: chain F4 residue 260 THR Chi-restraints excluded: chain F4 residue 321 MET Chi-restraints excluded: chain F4 residue 332 MET Chi-restraints excluded: chain F4 residue 337 GLN Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 57 MET Chi-restraints excluded: chain F5 residue 67 THR Chi-restraints excluded: chain F5 residue 83 THR Chi-restraints excluded: chain F5 residue 86 THR Chi-restraints excluded: chain F5 residue 110 GLU Chi-restraints excluded: chain F5 residue 147 THR Chi-restraints excluded: chain F5 residue 187 GLU Chi-restraints excluded: chain F5 residue 199 LYS Chi-restraints excluded: chain F5 residue 281 SER Chi-restraints excluded: chain F5 residue 282 CYS Chi-restraints excluded: chain F5 residue 310 LEU Chi-restraints excluded: chain F5 residue 357 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 141 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 3 optimal weight: 0.0970 chunk 153 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 114 optimal weight: 0.0570 chunk 119 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 163 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 71 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 = 0.3534 r_free = 0.3534 target = 0.147941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.118775 restraints weight = 13931.385| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.64 r_work: 0.2998 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14095 Z= 0.107 Angle : 0.557 5.612 19240 Z= 0.280 Chirality : 0.042 0.124 2155 Planarity : 0.004 0.028 2510 Dihedral : 5.489 53.105 1898 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 5.21 % Allowed : 25.27 % Favored : 69.52 % 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: -1.45 (0.20), residues: 1755 helix: -0.08 (0.57), residues: 85 sheet: 0.26 (0.25), residues: 460 loop : -1.64 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGF2 313 TYR 0.010 0.001 TYRF4 239 PHE 0.010 0.002 PHEF1 255 TRP 0.012 0.001 TRPF1 299 HIS 0.003 0.001 HISF4 298 Details of bonding type rmsd covalent geometry : bond 0.00263 (14090) covalent geometry : angle 0.55738 (19230) SS BOND : bond 0.00057 ( 5) SS BOND : angle 0.21663 ( 10) hydrogen bonds : bond 0.02477 ( 355) hydrogen bonds : angle 4.54128 ( 1008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 254 time to evaluate : 0.527 Fit side-chains REVERT: F1 21 ARG cc_start: 0.8107 (mmt-90) cc_final: 0.7655 (mtt180) REVERT: F1 57 MET cc_start: 0.7190 (mtp) cc_final: 0.6912 (mtp) REVERT: F1 85 ASP cc_start: 0.8492 (t70) cc_final: 0.8150 (t0) REVERT: F1 187 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7959 (mm-30) REVERT: F1 199 LYS cc_start: 0.8519 (mtmt) cc_final: 0.7915 (mptt) REVERT: F1 215 LYS cc_start: 0.8531 (mttm) cc_final: 0.8217 (mtpt) REVERT: F1 254 GLN cc_start: 0.8998 (mt0) cc_final: 0.8654 (mp10) REVERT: F1 292 ARG cc_start: 0.7892 (ttt180) cc_final: 0.7675 (mtt-85) REVERT: F1 316 LYS cc_start: 0.6476 (mttp) cc_final: 0.4873 (mmtm) REVERT: F1 321 MET cc_start: 0.6020 (mmt) cc_final: 0.5759 (mmm) REVERT: F1 332 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6520 (tmt) REVERT: F2 57 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.6432 (ttm) REVERT: F2 112 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8104 (mp) REVERT: F2 158 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8421 (mt-10) REVERT: F2 215 LYS cc_start: 0.8468 (mttm) cc_final: 0.8197 (mtpt) REVERT: F2 316 LYS cc_start: 0.6099 (mttp) cc_final: 0.4561 (tppt) REVERT: F2 337 GLN cc_start: 0.6922 (OUTLIER) cc_final: 0.6598 (mt0) REVERT: F2 363 ASP cc_start: 0.7116 (t70) cc_final: 0.6799 (t0) REVERT: F3 21 ARG cc_start: 0.8141 (mmp80) cc_final: 0.7564 (mtt-85) REVERT: F3 111 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.6860 (m-30) REVERT: F3 158 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8229 (mt-10) REVERT: F3 187 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8271 (mm-30) REVERT: F3 254 GLN cc_start: 0.8885 (mt0) cc_final: 0.8435 (mp10) REVERT: F3 316 LYS cc_start: 0.6044 (mttp) cc_final: 0.4408 (mmtm) REVERT: F3 337 GLN cc_start: 0.6715 (OUTLIER) cc_final: 0.6302 (mt0) REVERT: F3 363 ASP cc_start: 0.7378 (t0) cc_final: 0.7178 (t0) REVERT: F4 57 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7248 (mmm) REVERT: F4 91 GLU cc_start: 0.7128 (tp30) cc_final: 0.6864 (tp30) REVERT: F4 158 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8505 (mt-10) REVERT: F4 173 ASP cc_start: 0.8425 (m-30) cc_final: 0.8191 (m-30) REVERT: F4 184 LYS cc_start: 0.8419 (mttp) cc_final: 0.8041 (mtmt) REVERT: F4 316 LYS cc_start: 0.6165 (mttp) cc_final: 0.4544 (tptt) REVERT: F4 332 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6411 (tmm) REVERT: F4 363 ASP cc_start: 0.7396 (t70) cc_final: 0.7106 (t0) REVERT: F5 57 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.6914 (ttm) REVERT: F5 85 ASP cc_start: 0.8558 (t70) cc_final: 0.8178 (t0) REVERT: F5 91 GLU cc_start: 0.7145 (tp30) cc_final: 0.6877 (tp30) REVERT: F5 110 GLU cc_start: 0.6196 (OUTLIER) cc_final: 0.5981 (pt0) REVERT: F5 187 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7837 (mm-30) REVERT: F5 215 LYS cc_start: 0.8462 (mttm) cc_final: 0.8250 (mttt) REVERT: F5 316 LYS cc_start: 0.6379 (mttp) cc_final: 0.4727 (tptt) outliers start: 81 outliers final: 49 residues processed: 302 average time/residue: 0.5819 time to fit residues: 192.8154 Evaluate side-chains 290 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 230 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 67 THR Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 107 MET Chi-restraints excluded: chain F1 residue 147 THR Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 252 VAL Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 332 MET Chi-restraints excluded: chain F1 residue 357 THR Chi-restraints excluded: chain F2 residue 36 VAL Chi-restraints excluded: chain F2 residue 57 MET Chi-restraints excluded: chain F2 residue 65 SER Chi-restraints excluded: chain F2 residue 67 THR Chi-restraints excluded: chain F2 residue 112 LEU Chi-restraints excluded: chain F2 residue 154 SER Chi-restraints excluded: chain F2 residue 253 LEU Chi-restraints excluded: chain F2 residue 281 SER Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 296 VAL Chi-restraints excluded: chain F2 residue 319 TYR Chi-restraints excluded: chain F2 residue 337 GLN Chi-restraints excluded: chain F2 residue 357 THR Chi-restraints excluded: chain F3 residue 36 VAL Chi-restraints excluded: chain F3 residue 67 THR Chi-restraints excluded: chain F3 residue 83 THR Chi-restraints excluded: chain F3 residue 111 ASP Chi-restraints excluded: chain F3 residue 147 THR Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 208 LEU Chi-restraints excluded: chain F3 residue 281 SER Chi-restraints excluded: chain F3 residue 282 CYS Chi-restraints excluded: chain F3 residue 321 MET Chi-restraints excluded: chain F3 residue 337 GLN Chi-restraints excluded: chain F4 residue 36 VAL Chi-restraints excluded: chain F4 residue 57 MET Chi-restraints excluded: chain F4 residue 65 SER Chi-restraints excluded: chain F4 residue 79 ILE Chi-restraints excluded: chain F4 residue 86 THR Chi-restraints excluded: chain F4 residue 147 THR Chi-restraints excluded: chain F4 residue 154 SER Chi-restraints excluded: chain F4 residue 190 VAL Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 208 LEU Chi-restraints excluded: chain F4 residue 253 LEU Chi-restraints excluded: chain F4 residue 260 THR Chi-restraints excluded: chain F4 residue 281 SER Chi-restraints excluded: chain F4 residue 332 MET Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 57 MET Chi-restraints excluded: chain F5 residue 67 THR Chi-restraints excluded: chain F5 residue 83 THR Chi-restraints excluded: chain F5 residue 86 THR Chi-restraints excluded: chain F5 residue 110 GLU Chi-restraints excluded: chain F5 residue 187 GLU Chi-restraints excluded: chain F5 residue 199 LYS Chi-restraints excluded: chain F5 residue 281 SER Chi-restraints excluded: chain F5 residue 282 CYS Chi-restraints excluded: chain F5 residue 296 VAL Chi-restraints excluded: chain F5 residue 357 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 64 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 317 ASN ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.147105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.118556 restraints weight = 13887.458| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.59 r_work: 0.2987 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14095 Z= 0.116 Angle : 0.563 5.739 19240 Z= 0.282 Chirality : 0.042 0.125 2155 Planarity : 0.004 0.028 2510 Dihedral : 5.203 49.986 1894 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.89 % Allowed : 26.37 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.30 (0.20), residues: 1755 helix: 0.26 (0.59), residues: 85 sheet: 0.34 (0.25), residues: 460 loop : -1.54 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGF2 313 TYR 0.011 0.001 TYRF2 239 PHE 0.010 0.002 PHEF5 306 TRP 0.011 0.001 TRPF4 299 HIS 0.003 0.001 HISF5 298 Details of bonding type rmsd covalent geometry : bond 0.00288 (14090) covalent geometry : angle 0.56342 (19230) SS BOND : bond 0.00064 ( 5) SS BOND : angle 0.23388 ( 10) hydrogen bonds : bond 0.02526 ( 355) hydrogen bonds : angle 4.55408 ( 1008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 234 time to evaluate : 0.542 Fit side-chains REVERT: F1 57 MET cc_start: 0.7205 (mtp) cc_final: 0.6918 (mtp) REVERT: F1 85 ASP cc_start: 0.8476 (t70) cc_final: 0.8127 (t0) REVERT: F1 119 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8902 (mtp) REVERT: F1 184 LYS cc_start: 0.7974 (mppt) cc_final: 0.7629 (pttt) REVERT: F1 187 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7984 (mm-30) REVERT: F1 199 LYS cc_start: 0.8505 (mtmt) cc_final: 0.7907 (mptt) REVERT: F1 215 LYS cc_start: 0.8557 (mttm) cc_final: 0.8205 (mtpt) REVERT: F1 254 GLN cc_start: 0.8934 (mt0) cc_final: 0.8579 (mp10) REVERT: F1 316 LYS cc_start: 0.6480 (mttp) cc_final: 0.4862 (mmtm) REVERT: F1 321 MET cc_start: 0.6076 (mmt) cc_final: 0.5764 (mmm) REVERT: F2 57 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.6601 (ttm) REVERT: F2 112 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8056 (mp) REVERT: F2 158 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8448 (mt-10) REVERT: F2 215 LYS cc_start: 0.8487 (mttm) cc_final: 0.8204 (mtpt) REVERT: F2 316 LYS cc_start: 0.6088 (mttp) cc_final: 0.4572 (tppt) REVERT: F2 363 ASP cc_start: 0.7030 (t70) cc_final: 0.6686 (t0) REVERT: F3 21 ARG cc_start: 0.8199 (mmp80) cc_final: 0.7548 (mtt-85) REVERT: F3 187 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8368 (mp0) REVERT: F3 254 GLN cc_start: 0.8885 (mt0) cc_final: 0.8429 (mt0) REVERT: F3 316 LYS cc_start: 0.6041 (mttp) cc_final: 0.4361 (mmtm) REVERT: F3 363 ASP cc_start: 0.7298 (t0) cc_final: 0.7077 (t0) REVERT: F4 57 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7175 (mmm) REVERT: F4 91 GLU cc_start: 0.7158 (tp30) cc_final: 0.6862 (tp30) REVERT: F4 158 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8540 (mt-10) REVERT: F4 173 ASP cc_start: 0.8433 (m-30) cc_final: 0.8201 (m-30) REVERT: F4 184 LYS cc_start: 0.8443 (mttp) cc_final: 0.7968 (pttt) REVERT: F4 316 LYS cc_start: 0.6192 (mttp) cc_final: 0.4524 (tptt) REVERT: F4 332 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6432 (tmm) REVERT: F4 337 GLN cc_start: 0.6897 (OUTLIER) cc_final: 0.6633 (mt0) REVERT: F4 363 ASP cc_start: 0.7360 (t70) cc_final: 0.7085 (t0) REVERT: F5 57 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.6750 (ttm) REVERT: F5 85 ASP cc_start: 0.8563 (t70) cc_final: 0.8299 (t0) REVERT: F5 91 GLU cc_start: 0.7212 (tp30) cc_final: 0.6941 (tp30) REVERT: F5 110 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5997 (pt0) REVERT: F5 187 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7846 (mm-30) REVERT: F5 215 LYS cc_start: 0.8482 (mttm) cc_final: 0.8263 (mttt) REVERT: F5 316 LYS cc_start: 0.6368 (mttp) cc_final: 0.4680 (tptt) REVERT: F5 321 MET cc_start: 0.5785 (mmt) cc_final: 0.5488 (mmm) outliers start: 76 outliers final: 45 residues processed: 281 average time/residue: 0.5938 time to fit residues: 182.5083 Evaluate side-chains 277 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 222 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 36 VAL Chi-restraints excluded: chain F1 residue 67 THR Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 107 MET Chi-restraints excluded: chain F1 residue 119 MET Chi-restraints excluded: chain F1 residue 147 THR Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 187 GLU Chi-restraints excluded: chain F1 residue 252 VAL Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 357 THR Chi-restraints excluded: chain F2 residue 36 VAL Chi-restraints excluded: chain F2 residue 57 MET Chi-restraints excluded: chain F2 residue 67 THR Chi-restraints excluded: chain F2 residue 112 LEU Chi-restraints excluded: chain F2 residue 154 SER Chi-restraints excluded: chain F2 residue 253 LEU Chi-restraints excluded: chain F2 residue 281 SER Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 296 VAL Chi-restraints excluded: chain F2 residue 319 TYR Chi-restraints excluded: chain F2 residue 357 THR Chi-restraints excluded: chain F3 residue 36 VAL Chi-restraints excluded: chain F3 residue 67 THR Chi-restraints excluded: chain F3 residue 83 THR Chi-restraints excluded: chain F3 residue 86 THR Chi-restraints excluded: chain F3 residue 147 THR Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 208 LEU Chi-restraints excluded: chain F3 residue 281 SER Chi-restraints excluded: chain F3 residue 282 CYS Chi-restraints excluded: chain F4 residue 36 VAL Chi-restraints excluded: chain F4 residue 57 MET Chi-restraints excluded: chain F4 residue 65 SER Chi-restraints excluded: chain F4 residue 67 THR Chi-restraints excluded: chain F4 residue 154 SER Chi-restraints excluded: chain F4 residue 190 VAL Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 208 LEU Chi-restraints excluded: chain F4 residue 253 LEU Chi-restraints excluded: chain F4 residue 260 THR Chi-restraints excluded: chain F4 residue 281 SER Chi-restraints excluded: chain F4 residue 332 MET Chi-restraints excluded: chain F4 residue 337 GLN Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 57 MET Chi-restraints excluded: chain F5 residue 67 THR Chi-restraints excluded: chain F5 residue 110 GLU Chi-restraints excluded: chain F5 residue 187 GLU Chi-restraints excluded: chain F5 residue 281 SER Chi-restraints excluded: chain F5 residue 282 CYS Chi-restraints excluded: chain F5 residue 296 VAL Chi-restraints excluded: chain F5 residue 310 LEU Chi-restraints excluded: chain F5 residue 357 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 22 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 128 optimal weight: 0.0970 chunk 39 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 71 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 = 0.3473 r_free = 0.3473 target = 0.142754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.111420 restraints weight = 13679.635| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.70 r_work: 0.2855 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14095 Z= 0.153 Angle : 0.603 6.032 19240 Z= 0.303 Chirality : 0.043 0.127 2155 Planarity : 0.005 0.030 2510 Dihedral : 5.363 48.197 1892 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 4.95 % Allowed : 26.30 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.26 (0.20), residues: 1755 helix: 0.45 (0.60), residues: 85 sheet: 0.35 (0.25), residues: 460 loop : -1.52 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGF2 313 TYR 0.013 0.001 TYRF4 239 PHE 0.014 0.002 PHEF2 306 TRP 0.011 0.002 TRPF4 299 HIS 0.004 0.001 HISF5 298 Details of bonding type rmsd covalent geometry : bond 0.00379 (14090) covalent geometry : angle 0.60361 (19230) SS BOND : bond 0.00095 ( 5) SS BOND : angle 0.29636 ( 10) hydrogen bonds : bond 0.02756 ( 355) hydrogen bonds : angle 4.82496 ( 1008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 230 time to evaluate : 0.559 Fit side-chains REVERT: F1 57 MET cc_start: 0.7415 (mtp) cc_final: 0.7136 (mtp) REVERT: F1 85 ASP cc_start: 0.8503 (t70) cc_final: 0.8165 (t0) REVERT: F1 119 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8928 (mtp) REVERT: F1 187 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7985 (mm-30) REVERT: F1 199 LYS cc_start: 0.8514 (mtmt) cc_final: 0.7900 (mptt) REVERT: F1 215 LYS cc_start: 0.8681 (mttm) cc_final: 0.8390 (mttp) REVERT: F1 254 GLN cc_start: 0.9032 (mt0) cc_final: 0.8689 (mp10) REVERT: F1 316 LYS cc_start: 0.6610 (mttp) cc_final: 0.4938 (mmtm) REVERT: F2 57 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.6919 (ttm) REVERT: F2 158 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8501 (mt-10) REVERT: F2 215 LYS cc_start: 0.8539 (mttm) cc_final: 0.8269 (mttt) REVERT: F2 316 LYS cc_start: 0.6273 (mttp) cc_final: 0.4648 (tppt) REVERT: F2 321 MET cc_start: 0.5664 (mmt) cc_final: 0.5453 (mmm) REVERT: F2 363 ASP cc_start: 0.7056 (t70) cc_final: 0.6780 (t0) REVERT: F3 21 ARG cc_start: 0.8246 (mmp80) cc_final: 0.7630 (mtt-85) REVERT: F3 187 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8369 (mp0) REVERT: F3 254 GLN cc_start: 0.8969 (mt0) cc_final: 0.8539 (mt0) REVERT: F3 286 MET cc_start: 0.9024 (mmm) cc_final: 0.8807 (mmm) REVERT: F3 316 LYS cc_start: 0.6160 (mttp) cc_final: 0.4461 (mmtm) REVERT: F3 337 GLN cc_start: 0.6748 (OUTLIER) cc_final: 0.6372 (mt0) REVERT: F3 363 ASP cc_start: 0.7365 (t0) cc_final: 0.7087 (t0) REVERT: F4 57 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7368 (mmm) REVERT: F4 91 GLU cc_start: 0.7400 (tp30) cc_final: 0.7109 (tp30) REVERT: F4 158 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8699 (mt-10) REVERT: F4 173 ASP cc_start: 0.8538 (m-30) cc_final: 0.8297 (m-30) REVERT: F4 184 LYS cc_start: 0.8491 (mttp) cc_final: 0.8048 (mtmt) REVERT: F4 316 LYS cc_start: 0.6345 (mttp) cc_final: 0.4714 (mmtm) REVERT: F4 332 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6548 (tmm) REVERT: F4 337 GLN cc_start: 0.6960 (OUTLIER) cc_final: 0.6656 (mt0) REVERT: F4 341 MET cc_start: 0.9133 (mmt) cc_final: 0.8013 (mmt) REVERT: F4 363 ASP cc_start: 0.7346 (t70) cc_final: 0.7084 (t0) REVERT: F5 57 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.6851 (ttm) REVERT: F5 91 GLU cc_start: 0.7294 (tp30) cc_final: 0.7040 (tp30) REVERT: F5 110 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6202 (pt0) REVERT: F5 187 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7906 (mm-30) REVERT: F5 215 LYS cc_start: 0.8508 (mttm) cc_final: 0.8264 (mttp) REVERT: F5 316 LYS cc_start: 0.6475 (mttp) cc_final: 0.4733 (tptt) outliers start: 77 outliers final: 52 residues processed: 274 average time/residue: 0.5827 time to fit residues: 175.0158 Evaluate side-chains 285 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 223 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 36 VAL Chi-restraints excluded: chain F1 residue 67 THR Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 107 MET Chi-restraints excluded: chain F1 residue 119 MET Chi-restraints excluded: chain F1 residue 147 THR Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 187 GLU Chi-restraints excluded: chain F1 residue 252 VAL Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 357 THR Chi-restraints excluded: chain F2 residue 36 VAL Chi-restraints excluded: chain F2 residue 57 MET Chi-restraints excluded: chain F2 residue 65 SER Chi-restraints excluded: chain F2 residue 67 THR Chi-restraints excluded: chain F2 residue 154 SER Chi-restraints excluded: chain F2 residue 253 LEU Chi-restraints excluded: chain F2 residue 259 LEU Chi-restraints excluded: chain F2 residue 281 SER Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 296 VAL Chi-restraints excluded: chain F2 residue 319 TYR Chi-restraints excluded: chain F2 residue 357 THR Chi-restraints excluded: chain F3 residue 36 VAL Chi-restraints excluded: chain F3 residue 67 THR Chi-restraints excluded: chain F3 residue 83 THR Chi-restraints excluded: chain F3 residue 86 THR Chi-restraints excluded: chain F3 residue 146 ASP Chi-restraints excluded: chain F3 residue 147 THR Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 208 LEU Chi-restraints excluded: chain F3 residue 259 LEU Chi-restraints excluded: chain F3 residue 281 SER Chi-restraints excluded: chain F3 residue 282 CYS Chi-restraints excluded: chain F3 residue 337 GLN Chi-restraints excluded: chain F3 residue 350 GLU Chi-restraints excluded: chain F4 residue 36 VAL Chi-restraints excluded: chain F4 residue 57 MET Chi-restraints excluded: chain F4 residue 65 SER Chi-restraints excluded: chain F4 residue 67 THR Chi-restraints excluded: chain F4 residue 86 THR Chi-restraints excluded: chain F4 residue 147 THR Chi-restraints excluded: chain F4 residue 154 SER Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 208 LEU Chi-restraints excluded: chain F4 residue 253 LEU Chi-restraints excluded: chain F4 residue 260 THR Chi-restraints excluded: chain F4 residue 332 MET Chi-restraints excluded: chain F4 residue 337 GLN Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 57 MET Chi-restraints excluded: chain F5 residue 67 THR Chi-restraints excluded: chain F5 residue 110 GLU Chi-restraints excluded: chain F5 residue 147 THR Chi-restraints excluded: chain F5 residue 187 GLU Chi-restraints excluded: chain F5 residue 199 LYS Chi-restraints excluded: chain F5 residue 281 SER Chi-restraints excluded: chain F5 residue 282 CYS Chi-restraints excluded: chain F5 residue 296 VAL Chi-restraints excluded: chain F5 residue 310 LEU Chi-restraints excluded: chain F5 residue 357 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 91 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 146 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 345 ASN ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.141681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.109876 restraints weight = 13580.645| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.73 r_work: 0.2828 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14095 Z= 0.174 Angle : 0.625 6.110 19240 Z= 0.314 Chirality : 0.044 0.132 2155 Planarity : 0.005 0.033 2510 Dihedral : 5.524 50.279 1892 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 5.21 % Allowed : 26.17 % Favored : 68.62 % 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: -1.20 (0.20), residues: 1755 helix: 0.54 (0.60), residues: 85 sheet: 0.51 (0.25), residues: 450 loop : -1.52 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGF1 292 TYR 0.014 0.001 TYRF4 239 PHE 0.016 0.003 PHEF2 306 TRP 0.012 0.002 TRPF4 299 HIS 0.004 0.001 HISF5 298 Details of bonding type rmsd covalent geometry : bond 0.00430 (14090) covalent geometry : angle 0.62500 (19230) SS BOND : bond 0.00102 ( 5) SS BOND : angle 0.38409 ( 10) hydrogen bonds : bond 0.02849 ( 355) hydrogen bonds : angle 4.91026 ( 1008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 216 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: F1 57 MET cc_start: 0.7459 (mtp) cc_final: 0.7175 (mtp) REVERT: F1 85 ASP cc_start: 0.8559 (t70) cc_final: 0.8206 (t0) REVERT: F1 119 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8948 (mtp) REVERT: F1 187 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7998 (mm-30) REVERT: F1 199 LYS cc_start: 0.8475 (mtmt) cc_final: 0.7853 (mptt) REVERT: F1 215 LYS cc_start: 0.8676 (mttm) cc_final: 0.8383 (mttp) REVERT: F1 316 LYS cc_start: 0.6624 (mttp) cc_final: 0.4938 (mmtm) REVERT: F2 57 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.6993 (ttm) REVERT: F2 111 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7208 (t70) REVERT: F2 158 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8533 (mt-10) REVERT: F2 215 LYS cc_start: 0.8537 (mttm) cc_final: 0.8271 (mttt) REVERT: F2 316 LYS cc_start: 0.6286 (mttp) cc_final: 0.4666 (tppt) REVERT: F2 321 MET cc_start: 0.5683 (mmt) cc_final: 0.5480 (mmm) REVERT: F2 363 ASP cc_start: 0.7071 (t70) cc_final: 0.6798 (t0) REVERT: F3 119 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8743 (ptm) REVERT: F3 187 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8404 (mp0) REVERT: F3 254 GLN cc_start: 0.8996 (mt0) cc_final: 0.8562 (mt0) REVERT: F3 286 MET cc_start: 0.8995 (mmm) cc_final: 0.8723 (mmm) REVERT: F3 292 ARG cc_start: 0.8005 (ttt180) cc_final: 0.7648 (mtt180) REVERT: F3 316 LYS cc_start: 0.6167 (mttp) cc_final: 0.4454 (mmtm) REVERT: F3 337 GLN cc_start: 0.6735 (OUTLIER) cc_final: 0.6340 (mt0) REVERT: F3 363 ASP cc_start: 0.7367 (t0) cc_final: 0.7149 (t0) REVERT: F3 366 MET cc_start: 0.6329 (mmp) cc_final: 0.5996 (mmm) REVERT: F4 57 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7453 (mmm) REVERT: F4 91 GLU cc_start: 0.7399 (tp30) cc_final: 0.7105 (tp30) REVERT: F4 158 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8732 (mt-10) REVERT: F4 173 ASP cc_start: 0.8556 (m-30) cc_final: 0.8321 (m-30) REVERT: F4 184 LYS cc_start: 0.8531 (mttp) cc_final: 0.8111 (mtmt) REVERT: F4 316 LYS cc_start: 0.6384 (mttp) cc_final: 0.4660 (mmtm) REVERT: F4 321 MET cc_start: 0.6105 (mmt) cc_final: 0.5882 (mmm) REVERT: F4 332 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6788 (tmm) REVERT: F4 337 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6635 (mt0) REVERT: F4 341 MET cc_start: 0.9148 (mmt) cc_final: 0.8100 (mmt) REVERT: F4 363 ASP cc_start: 0.7316 (t70) cc_final: 0.7067 (t0) REVERT: F5 57 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.6750 (ttm) REVERT: F5 91 GLU cc_start: 0.7273 (tp30) cc_final: 0.7001 (tp30) REVERT: F5 110 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6553 (pt0) REVERT: F5 187 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7921 (mm-30) REVERT: F5 215 LYS cc_start: 0.8543 (mttm) cc_final: 0.8310 (mttm) REVERT: F5 316 LYS cc_start: 0.6520 (mttp) cc_final: 0.4799 (tptt) outliers start: 81 outliers final: 56 residues processed: 267 average time/residue: 0.5648 time to fit residues: 165.3375 Evaluate side-chains 283 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 215 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 36 VAL Chi-restraints excluded: chain F1 residue 67 THR Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 107 MET Chi-restraints excluded: chain F1 residue 119 MET Chi-restraints excluded: chain F1 residue 147 THR Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 187 GLU Chi-restraints excluded: chain F1 residue 207 VAL Chi-restraints excluded: chain F1 residue 252 VAL Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 357 THR Chi-restraints excluded: chain F2 residue 36 VAL Chi-restraints excluded: chain F2 residue 57 MET Chi-restraints excluded: chain F2 residue 67 THR Chi-restraints excluded: chain F2 residue 86 THR Chi-restraints excluded: chain F2 residue 111 ASP Chi-restraints excluded: chain F2 residue 154 SER Chi-restraints excluded: chain F2 residue 207 VAL Chi-restraints excluded: chain F2 residue 253 LEU Chi-restraints excluded: chain F2 residue 259 LEU Chi-restraints excluded: chain F2 residue 281 SER Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 296 VAL Chi-restraints excluded: chain F2 residue 319 TYR Chi-restraints excluded: chain F2 residue 324 LEU Chi-restraints excluded: chain F2 residue 357 THR Chi-restraints excluded: chain F3 residue 36 VAL Chi-restraints excluded: chain F3 residue 67 THR Chi-restraints excluded: chain F3 residue 83 THR Chi-restraints excluded: chain F3 residue 86 THR Chi-restraints excluded: chain F3 residue 119 MET Chi-restraints excluded: chain F3 residue 146 ASP Chi-restraints excluded: chain F3 residue 147 THR Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 208 LEU Chi-restraints excluded: chain F3 residue 259 LEU Chi-restraints excluded: chain F3 residue 281 SER Chi-restraints excluded: chain F3 residue 282 CYS Chi-restraints excluded: chain F3 residue 337 GLN Chi-restraints excluded: chain F3 residue 350 GLU Chi-restraints excluded: chain F4 residue 36 VAL Chi-restraints excluded: chain F4 residue 57 MET Chi-restraints excluded: chain F4 residue 67 THR Chi-restraints excluded: chain F4 residue 86 THR Chi-restraints excluded: chain F4 residue 147 THR Chi-restraints excluded: chain F4 residue 154 SER Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 211 ILE Chi-restraints excluded: chain F4 residue 253 LEU Chi-restraints excluded: chain F4 residue 260 THR Chi-restraints excluded: chain F4 residue 332 MET Chi-restraints excluded: chain F4 residue 337 GLN Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 57 MET Chi-restraints excluded: chain F5 residue 67 THR Chi-restraints excluded: chain F5 residue 86 THR Chi-restraints excluded: chain F5 residue 110 GLU Chi-restraints excluded: chain F5 residue 112 LEU Chi-restraints excluded: chain F5 residue 147 THR Chi-restraints excluded: chain F5 residue 187 GLU Chi-restraints excluded: chain F5 residue 199 LYS Chi-restraints excluded: chain F5 residue 207 VAL Chi-restraints excluded: chain F5 residue 281 SER Chi-restraints excluded: chain F5 residue 282 CYS Chi-restraints excluded: chain F5 residue 296 VAL Chi-restraints excluded: chain F5 residue 357 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 133 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 345 ASN ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.143085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.113898 restraints weight = 13919.377| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.64 r_work: 0.2922 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14095 Z= 0.154 Angle : 0.606 6.980 19240 Z= 0.304 Chirality : 0.043 0.128 2155 Planarity : 0.005 0.035 2510 Dihedral : 5.438 52.399 1892 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 4.76 % Allowed : 26.37 % Favored : 68.87 % 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: -1.14 (0.20), residues: 1755 helix: 0.65 (0.60), residues: 85 sheet: 0.53 (0.25), residues: 450 loop : -1.47 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGF1 292 TYR 0.013 0.001 TYRF4 239 PHE 0.014 0.002 PHEF2 306 TRP 0.012 0.002 TRPF4 299 HIS 0.004 0.001 HISF5 298 Details of bonding type rmsd covalent geometry : bond 0.00380 (14090) covalent geometry : angle 0.60622 (19230) SS BOND : bond 0.00073 ( 5) SS BOND : angle 0.33500 ( 10) hydrogen bonds : bond 0.02740 ( 355) hydrogen bonds : angle 4.81931 ( 1008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 227 time to evaluate : 0.659 Fit side-chains REVERT: F1 57 MET cc_start: 0.7369 (mtp) cc_final: 0.7073 (mtp) REVERT: F1 85 ASP cc_start: 0.8553 (t70) cc_final: 0.8190 (t0) REVERT: F1 187 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7991 (mm-30) REVERT: F1 199 LYS cc_start: 0.8492 (mtmt) cc_final: 0.7924 (mptt) REVERT: F1 215 LYS cc_start: 0.8640 (mttm) cc_final: 0.8366 (mttp) REVERT: F1 254 GLN cc_start: 0.8960 (mt0) cc_final: 0.8602 (mp10) REVERT: F1 316 LYS cc_start: 0.6639 (mttp) cc_final: 0.4994 (mmtm) REVERT: F2 57 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.6906 (ttm) REVERT: F2 158 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8449 (mt-10) REVERT: F2 215 LYS cc_start: 0.8504 (mttm) cc_final: 0.8241 (mttt) REVERT: F2 316 LYS cc_start: 0.6197 (mttp) cc_final: 0.4640 (tppt) REVERT: F2 321 MET cc_start: 0.5790 (mmt) cc_final: 0.5550 (mmm) REVERT: F2 363 ASP cc_start: 0.7080 (t70) cc_final: 0.6798 (t0) REVERT: F3 119 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8661 (ptm) REVERT: F3 187 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8366 (mp0) REVERT: F3 254 GLN cc_start: 0.8873 (mt0) cc_final: 0.8401 (mt0) REVERT: F3 286 MET cc_start: 0.8921 (mmm) cc_final: 0.8672 (mmm) REVERT: F3 292 ARG cc_start: 0.8050 (ttt180) cc_final: 0.7679 (mtt180) REVERT: F3 316 LYS cc_start: 0.6102 (mttp) cc_final: 0.4498 (mmtm) REVERT: F3 337 GLN cc_start: 0.6668 (OUTLIER) cc_final: 0.6267 (mt0) REVERT: F3 363 ASP cc_start: 0.7403 (t0) cc_final: 0.7191 (t0) REVERT: F3 366 MET cc_start: 0.6291 (mmp) cc_final: 0.5957 (mmm) REVERT: F4 57 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7375 (mmm) REVERT: F4 91 GLU cc_start: 0.7163 (tp30) cc_final: 0.6885 (tp30) REVERT: F4 158 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8605 (mt-10) REVERT: F4 173 ASP cc_start: 0.8422 (m-30) cc_final: 0.8183 (m-30) REVERT: F4 184 LYS cc_start: 0.8548 (mttp) cc_final: 0.8161 (mtmt) REVERT: F4 316 LYS cc_start: 0.6298 (mttp) cc_final: 0.4717 (mmtm) REVERT: F4 321 MET cc_start: 0.6193 (mmt) cc_final: 0.5853 (mmm) REVERT: F4 332 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6686 (tmm) REVERT: F4 337 GLN cc_start: 0.6949 (OUTLIER) cc_final: 0.6665 (mt0) REVERT: F4 341 MET cc_start: 0.9148 (mmt) cc_final: 0.8007 (mmt) REVERT: F4 363 ASP cc_start: 0.7351 (t70) cc_final: 0.7088 (t0) REVERT: F5 57 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.6850 (ttm) REVERT: F5 91 GLU cc_start: 0.7196 (tp30) cc_final: 0.6961 (tp30) REVERT: F5 110 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6282 (pt0) REVERT: F5 187 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7900 (mm-30) REVERT: F5 215 LYS cc_start: 0.8535 (mttm) cc_final: 0.8295 (mttp) REVERT: F5 316 LYS cc_start: 0.6482 (mttp) cc_final: 0.4806 (tptt) REVERT: F5 350 GLU cc_start: 0.8354 (tt0) cc_final: 0.8115 (tt0) outliers start: 74 outliers final: 55 residues processed: 270 average time/residue: 0.5821 time to fit residues: 171.8644 Evaluate side-chains 288 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 223 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 36 VAL Chi-restraints excluded: chain F1 residue 67 THR Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 107 MET Chi-restraints excluded: chain F1 residue 147 THR Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 187 GLU Chi-restraints excluded: chain F1 residue 252 VAL Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 357 THR Chi-restraints excluded: chain F2 residue 36 VAL Chi-restraints excluded: chain F2 residue 57 MET Chi-restraints excluded: chain F2 residue 67 THR Chi-restraints excluded: chain F2 residue 86 THR Chi-restraints excluded: chain F2 residue 147 THR Chi-restraints excluded: chain F2 residue 154 SER Chi-restraints excluded: chain F2 residue 207 VAL Chi-restraints excluded: chain F2 residue 253 LEU Chi-restraints excluded: chain F2 residue 259 LEU Chi-restraints excluded: chain F2 residue 281 SER Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 296 VAL Chi-restraints excluded: chain F2 residue 319 TYR Chi-restraints excluded: chain F2 residue 357 THR Chi-restraints excluded: chain F3 residue 36 VAL Chi-restraints excluded: chain F3 residue 67 THR Chi-restraints excluded: chain F3 residue 83 THR Chi-restraints excluded: chain F3 residue 86 THR Chi-restraints excluded: chain F3 residue 119 MET Chi-restraints excluded: chain F3 residue 146 ASP Chi-restraints excluded: chain F3 residue 147 THR Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 208 LEU Chi-restraints excluded: chain F3 residue 259 LEU Chi-restraints excluded: chain F3 residue 281 SER Chi-restraints excluded: chain F3 residue 282 CYS Chi-restraints excluded: chain F3 residue 337 GLN Chi-restraints excluded: chain F4 residue 36 VAL Chi-restraints excluded: chain F4 residue 57 MET Chi-restraints excluded: chain F4 residue 67 THR Chi-restraints excluded: chain F4 residue 86 THR Chi-restraints excluded: chain F4 residue 147 THR Chi-restraints excluded: chain F4 residue 154 SER Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 208 LEU Chi-restraints excluded: chain F4 residue 211 ILE Chi-restraints excluded: chain F4 residue 253 LEU Chi-restraints excluded: chain F4 residue 260 THR Chi-restraints excluded: chain F4 residue 332 MET Chi-restraints excluded: chain F4 residue 337 GLN Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 57 MET Chi-restraints excluded: chain F5 residue 67 THR Chi-restraints excluded: chain F5 residue 86 THR Chi-restraints excluded: chain F5 residue 110 GLU Chi-restraints excluded: chain F5 residue 147 THR Chi-restraints excluded: chain F5 residue 187 GLU Chi-restraints excluded: chain F5 residue 199 LYS Chi-restraints excluded: chain F5 residue 207 VAL Chi-restraints excluded: chain F5 residue 211 ILE Chi-restraints excluded: chain F5 residue 281 SER Chi-restraints excluded: chain F5 residue 282 CYS Chi-restraints excluded: chain F5 residue 296 VAL Chi-restraints excluded: chain F5 residue 357 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 143 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 345 ASN ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.142420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.110783 restraints weight = 13648.467| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.68 r_work: 0.2847 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14095 Z= 0.155 Angle : 0.610 7.121 19240 Z= 0.306 Chirality : 0.043 0.209 2155 Planarity : 0.005 0.035 2510 Dihedral : 5.444 53.023 1892 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 4.37 % Allowed : 27.01 % Favored : 68.62 % 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: -1.10 (0.20), residues: 1755 helix: 0.72 (0.60), residues: 85 sheet: 0.54 (0.26), residues: 450 loop : -1.44 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGF1 292 TYR 0.013 0.001 TYRF4 239 PHE 0.014 0.002 PHEF2 306 TRP 0.012 0.002 TRPF4 299 HIS 0.004 0.001 HISF5 298 Details of bonding type rmsd covalent geometry : bond 0.00384 (14090) covalent geometry : angle 0.60967 (19230) SS BOND : bond 0.00064 ( 5) SS BOND : angle 0.33930 ( 10) hydrogen bonds : bond 0.02732 ( 355) hydrogen bonds : angle 4.82650 ( 1008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 224 time to evaluate : 0.406 Fit side-chains REVERT: F1 57 MET cc_start: 0.7424 (mtp) cc_final: 0.7138 (mtp) REVERT: F1 85 ASP cc_start: 0.8551 (t70) cc_final: 0.8186 (t0) REVERT: F1 187 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8003 (mm-30) REVERT: F1 199 LYS cc_start: 0.8495 (mtmt) cc_final: 0.7869 (mptt) REVERT: F1 215 LYS cc_start: 0.8667 (mttm) cc_final: 0.8373 (mttp) REVERT: F1 316 LYS cc_start: 0.6577 (mttp) cc_final: 0.4907 (mmtm) REVERT: F2 57 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.6851 (ttm) REVERT: F2 158 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8503 (mt-10) REVERT: F2 215 LYS cc_start: 0.8542 (mttm) cc_final: 0.8285 (mttt) REVERT: F2 316 LYS cc_start: 0.6181 (mttp) cc_final: 0.4633 (tppt) REVERT: F2 321 MET cc_start: 0.5972 (mmt) cc_final: 0.5759 (mmm) REVERT: F2 363 ASP cc_start: 0.7046 (t70) cc_final: 0.6766 (t0) REVERT: F3 119 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8675 (ptm) REVERT: F3 254 GLN cc_start: 0.8970 (mt0) cc_final: 0.8539 (mt0) REVERT: F3 286 MET cc_start: 0.8966 (mmm) cc_final: 0.8729 (mmm) REVERT: F3 292 ARG cc_start: 0.8005 (ttt180) cc_final: 0.7635 (mtt180) REVERT: F3 316 LYS cc_start: 0.6049 (mttp) cc_final: 0.4406 (mmtm) REVERT: F3 337 GLN cc_start: 0.6706 (OUTLIER) cc_final: 0.6319 (mt0) REVERT: F3 363 ASP cc_start: 0.7344 (t0) cc_final: 0.7114 (t0) REVERT: F3 366 MET cc_start: 0.6395 (mmp) cc_final: 0.6012 (mmm) REVERT: F4 57 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7451 (mmm) REVERT: F4 91 GLU cc_start: 0.7354 (tp30) cc_final: 0.7065 (tp30) REVERT: F4 158 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8697 (mt-10) REVERT: F4 173 ASP cc_start: 0.8519 (m-30) cc_final: 0.8287 (m-30) REVERT: F4 184 LYS cc_start: 0.8524 (mttp) cc_final: 0.8110 (mtmt) REVERT: F4 316 LYS cc_start: 0.6300 (mttp) cc_final: 0.4678 (mmtm) REVERT: F4 332 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6679 (tmm) REVERT: F4 337 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6659 (mt0) REVERT: F4 341 MET cc_start: 0.9164 (mmt) cc_final: 0.8030 (mmt) REVERT: F5 57 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.6736 (ttm) REVERT: F5 91 GLU cc_start: 0.7273 (tp30) cc_final: 0.7054 (tp30) REVERT: F5 110 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.6054 (pt0) REVERT: F5 187 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7904 (mm-30) REVERT: F5 215 LYS cc_start: 0.8509 (mttm) cc_final: 0.8254 (mttp) REVERT: F5 316 LYS cc_start: 0.6487 (mttp) cc_final: 0.4786 (tptt) REVERT: F5 350 GLU cc_start: 0.8458 (tt0) cc_final: 0.8220 (tt0) outliers start: 68 outliers final: 53 residues processed: 263 average time/residue: 0.5613 time to fit residues: 161.4861 Evaluate side-chains 284 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 221 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 36 VAL Chi-restraints excluded: chain F1 residue 67 THR Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 107 MET Chi-restraints excluded: chain F1 residue 147 THR Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 187 GLU Chi-restraints excluded: chain F1 residue 252 VAL Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 357 THR Chi-restraints excluded: chain F2 residue 36 VAL Chi-restraints excluded: chain F2 residue 57 MET Chi-restraints excluded: chain F2 residue 67 THR Chi-restraints excluded: chain F2 residue 86 THR Chi-restraints excluded: chain F2 residue 147 THR Chi-restraints excluded: chain F2 residue 154 SER Chi-restraints excluded: chain F2 residue 253 LEU Chi-restraints excluded: chain F2 residue 259 LEU Chi-restraints excluded: chain F2 residue 281 SER Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 296 VAL Chi-restraints excluded: chain F2 residue 319 TYR Chi-restraints excluded: chain F2 residue 357 THR Chi-restraints excluded: chain F3 residue 36 VAL Chi-restraints excluded: chain F3 residue 67 THR Chi-restraints excluded: chain F3 residue 83 THR Chi-restraints excluded: chain F3 residue 86 THR Chi-restraints excluded: chain F3 residue 119 MET Chi-restraints excluded: chain F3 residue 146 ASP Chi-restraints excluded: chain F3 residue 147 THR Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 208 LEU Chi-restraints excluded: chain F3 residue 259 LEU Chi-restraints excluded: chain F3 residue 281 SER Chi-restraints excluded: chain F3 residue 282 CYS Chi-restraints excluded: chain F3 residue 337 GLN Chi-restraints excluded: chain F4 residue 36 VAL Chi-restraints excluded: chain F4 residue 57 MET Chi-restraints excluded: chain F4 residue 67 THR Chi-restraints excluded: chain F4 residue 86 THR Chi-restraints excluded: chain F4 residue 147 THR Chi-restraints excluded: chain F4 residue 154 SER Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 208 LEU Chi-restraints excluded: chain F4 residue 211 ILE Chi-restraints excluded: chain F4 residue 253 LEU Chi-restraints excluded: chain F4 residue 260 THR Chi-restraints excluded: chain F4 residue 332 MET Chi-restraints excluded: chain F4 residue 337 GLN Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 57 MET Chi-restraints excluded: chain F5 residue 67 THR Chi-restraints excluded: chain F5 residue 86 THR Chi-restraints excluded: chain F5 residue 110 GLU Chi-restraints excluded: chain F5 residue 147 THR Chi-restraints excluded: chain F5 residue 187 GLU Chi-restraints excluded: chain F5 residue 199 LYS Chi-restraints excluded: chain F5 residue 207 VAL Chi-restraints excluded: chain F5 residue 281 SER Chi-restraints excluded: chain F5 residue 282 CYS Chi-restraints excluded: chain F5 residue 296 VAL Chi-restraints excluded: chain F5 residue 357 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 2 optimal weight: 5.9990 chunk 60 optimal weight: 0.0370 chunk 173 optimal weight: 0.0270 chunk 37 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 158 optimal weight: 0.0980 chunk 116 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 345 ASN ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 345 ASN ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.145269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.116235 restraints weight = 14004.518| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.66 r_work: 0.2945 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14095 Z= 0.123 Angle : 0.576 7.338 19240 Z= 0.288 Chirality : 0.042 0.194 2155 Planarity : 0.004 0.034 2510 Dihedral : 5.216 54.054 1892 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.99 % Allowed : 27.40 % Favored : 68.62 % 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: -1.35 (0.20), residues: 1755 helix: -1.05 (0.49), residues: 125 sheet: 0.43 (0.26), residues: 460 loop : -1.53 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGF2 313 TYR 0.011 0.001 TYRF4 239 PHE 0.010 0.002 PHEF2 306 TRP 0.013 0.002 TRPF3 299 HIS 0.003 0.001 HISF5 298 Details of bonding type rmsd covalent geometry : bond 0.00304 (14090) covalent geometry : angle 0.57600 (19230) SS BOND : bond 0.00044 ( 5) SS BOND : angle 0.23032 ( 10) hydrogen bonds : bond 0.02549 ( 355) hydrogen bonds : angle 4.63446 ( 1008) =============================================================================== Job complete usr+sys time: 5335.67 seconds wall clock time: 91 minutes 26.70 seconds (5486.70 seconds total)