Starting phenix.real_space_refine on Sun Apr 5 08:35:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z23_14456/04_2026/7z23_14456.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z23_14456/04_2026/7z23_14456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z23_14456/04_2026/7z23_14456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z23_14456/04_2026/7z23_14456.map" model { file = "/net/cci-nas-00/data/ceres_data/7z23_14456/04_2026/7z23_14456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z23_14456/04_2026/7z23_14456.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 48 5.16 5 C 6198 2.51 5 N 1446 2.21 5 O 1554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9246 Number of models: 1 Model: "" Number of chains: 1 Chain: "E" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Restraints were copied for chains: A, B, C, D, F Time building chain proxies: 1.37, per 1000 atoms: 0.15 Number of scatterers: 9246 At special positions: 0 Unit cell: (101.37, 105.294, 86.328, 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 48 16.00 O 1554 8.00 N 1446 7.00 C 6198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 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: 0.68 Conformation dependent library (CDL) restraints added in 411.3 milliseconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 77.8% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'E' and resid 3 through 15 removed outlier: 4.297A pdb=" N LEU E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 45 removed outlier: 4.404A pdb=" N TRP E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU E 42 " --> pdb=" O GLY E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 103 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 152 through 178 Processing helix chain 'E' and resid 202 through 235 Processing helix chain 'A' and resid 3 through 15 removed outlier: 4.298A pdb=" N LEU A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 45 removed outlier: 4.404A pdb=" N TRP A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 103 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 152 through 178 Processing helix chain 'A' and resid 202 through 235 Processing helix chain 'B' and resid 3 through 15 removed outlier: 4.298A pdb=" N LEU B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 45 removed outlier: 4.404A pdb=" N TRP B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 103 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 152 through 178 Processing helix chain 'B' and resid 202 through 235 Processing helix chain 'C' and resid 3 through 15 removed outlier: 4.297A pdb=" N LEU C 7 " --> pdb=" O ASP C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 45 removed outlier: 4.404A pdb=" N TRP C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU C 42 " --> pdb=" O GLY C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 103 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 152 through 178 Processing helix chain 'C' and resid 202 through 235 Processing helix chain 'D' and resid 3 through 15 removed outlier: 4.297A pdb=" N LEU D 7 " --> pdb=" O ASP D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 45 removed outlier: 4.404A pdb=" N TRP D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 103 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 152 through 178 Processing helix chain 'D' and resid 202 through 235 Processing helix chain 'F' and resid 3 through 15 removed outlier: 4.297A pdb=" N LEU F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 45 removed outlier: 4.404A pdb=" N TRP F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU F 42 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 52 Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 73 through 103 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 152 through 178 Processing helix chain 'F' and resid 202 through 235 Processing sheet with id=AA1, first strand: chain 'E' and resid 53 through 54 removed outlier: 4.532A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE E 199 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 4.532A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 199 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 removed outlier: 4.532A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE B 199 " --> pdb=" O ARG B 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 54 removed outlier: 4.532A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE C 199 " --> pdb=" O ARG C 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 53 through 54 removed outlier: 4.532A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE D 199 " --> pdb=" O ARG D 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 4.532A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE F 199 " --> pdb=" O ARG F 53 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 2034 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 0.95 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: 2676 1.34 - 1.46: 2079 1.46 - 1.58: 4689 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 9504 Sorted by residual: bond pdb=" C VAL D 87 " pdb=" N PRO D 88 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.72e+00 bond pdb=" C VAL E 87 " pdb=" N PRO E 88 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.68e+00 bond pdb=" C ASP C 190 " pdb=" N PRO C 191 " ideal model delta sigma weight residual 1.335 1.357 -0.023 1.19e-02 7.06e+03 3.58e+00 bond pdb=" C VAL C 87 " pdb=" N PRO C 88 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.28e-02 6.10e+03 3.54e+00 bond pdb=" C VAL F 87 " pdb=" N PRO F 88 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.28e-02 6.10e+03 3.50e+00 ... (remaining 9499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 11921 1.49 - 2.98: 772 2.98 - 4.47: 120 4.47 - 5.96: 75 5.96 - 7.46: 12 Bond angle restraints: 12900 Sorted by residual: angle pdb=" N ARG D 76 " pdb=" CA ARG D 76 " pdb=" C ARG D 76 " ideal model delta sigma weight residual 111.36 107.02 4.34 1.09e+00 8.42e-01 1.59e+01 angle pdb=" N ARG B 76 " pdb=" CA ARG B 76 " pdb=" C ARG B 76 " ideal model delta sigma weight residual 111.36 107.05 4.31 1.09e+00 8.42e-01 1.56e+01 angle pdb=" N ARG A 76 " pdb=" CA ARG A 76 " pdb=" C ARG A 76 " ideal model delta sigma weight residual 111.36 107.06 4.30 1.09e+00 8.42e-01 1.56e+01 angle pdb=" N ARG E 76 " pdb=" CA ARG E 76 " pdb=" C ARG E 76 " ideal model delta sigma weight residual 111.36 107.06 4.30 1.09e+00 8.42e-01 1.55e+01 angle pdb=" N ARG C 76 " pdb=" CA ARG C 76 " pdb=" C ARG C 76 " ideal model delta sigma weight residual 111.36 107.07 4.29 1.09e+00 8.42e-01 1.55e+01 ... (remaining 12895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 4824 15.94 - 31.87: 564 31.87 - 47.81: 114 47.81 - 63.75: 18 63.75 - 79.68: 12 Dihedral angle restraints: 5532 sinusoidal: 2196 harmonic: 3336 Sorted by residual: dihedral pdb=" CB CYS A 61 " pdb=" SG CYS A 61 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual 93.00 35.11 57.89 1 1.00e+01 1.00e-02 4.50e+01 dihedral pdb=" CB CYS D 61 " pdb=" SG CYS D 61 " pdb=" SG CYS D 192 " pdb=" CB CYS D 192 " ideal model delta sinusoidal sigma weight residual 93.00 35.13 57.87 1 1.00e+01 1.00e-02 4.49e+01 dihedral pdb=" CB CYS B 61 " pdb=" SG CYS B 61 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual 93.00 35.13 57.87 1 1.00e+01 1.00e-02 4.49e+01 ... (remaining 5529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1168 0.049 - 0.097: 236 0.097 - 0.146: 57 0.146 - 0.194: 4 0.194 - 0.243: 11 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CA TRP C 78 " pdb=" N TRP C 78 " pdb=" C TRP C 78 " pdb=" CB TRP C 78 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA TRP F 78 " pdb=" N TRP F 78 " pdb=" C TRP F 78 " pdb=" CB TRP F 78 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA TRP D 78 " pdb=" N TRP D 78 " pdb=" C TRP D 78 " pdb=" CB TRP D 78 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1473 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 212 " 0.020 2.00e-02 2.50e+03 1.93e-02 6.51e+00 pdb=" CG PHE C 212 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE C 212 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 212 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE C 212 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 212 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 212 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 212 " 0.021 2.00e-02 2.50e+03 1.93e-02 6.49e+00 pdb=" CG PHE B 212 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE B 212 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 212 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 212 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 212 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 212 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 212 " -0.021 2.00e-02 2.50e+03 1.92e-02 6.44e+00 pdb=" CG PHE D 212 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE D 212 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE D 212 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 212 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 212 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 212 " -0.002 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2502 2.80 - 3.33: 10130 3.33 - 3.85: 15635 3.85 - 4.38: 16709 4.38 - 4.90: 27744 Nonbonded interactions: 72720 Sorted by model distance: nonbonded pdb=" NH1 ARG B 76 " pdb=" O ALA C 40 " model vdw 2.280 3.120 nonbonded pdb=" NH1 ARG E 76 " pdb=" O ALA A 40 " model vdw 2.283 3.120 nonbonded pdb=" O SER B 86 " pdb=" OG1 THR B 89 " model vdw 2.283 3.040 nonbonded pdb=" O SER F 86 " pdb=" OG1 THR F 89 " model vdw 2.284 3.040 nonbonded pdb=" O SER D 86 " pdb=" OG1 THR D 89 " model vdw 2.284 3.040 ... (remaining 72715 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.300 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 0.004 0.033 9522 Z= 0.195 Angle : 0.921 7.456 12936 Z= 0.559 Chirality : 0.047 0.243 1476 Planarity : 0.006 0.055 1548 Dihedral : 14.001 79.684 3318 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.25), residues: 1110 helix: 0.28 (0.18), residues: 864 sheet: 0.15 (0.69), residues: 60 loop : -2.31 (0.36), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 76 TYR 0.009 0.001 TYR E 66 PHE 0.045 0.003 PHE C 212 TRP 0.017 0.003 TRP E 174 HIS 0.009 0.002 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9504) covalent geometry : angle 0.92160 (12900) SS BOND : bond 0.00147 ( 18) SS BOND : angle 0.83746 ( 36) hydrogen bonds : bond 0.09775 ( 684) hydrogen bonds : angle 5.50995 ( 2034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 100 MET cc_start: 0.9292 (mpp) cc_final: 0.9054 (mpp) REVERT: E 224 ASN cc_start: 0.9358 (p0) cc_final: 0.8820 (p0) REVERT: A 100 MET cc_start: 0.9243 (mpp) cc_final: 0.8990 (mpp) REVERT: A 166 GLU cc_start: 0.9379 (mt-10) cc_final: 0.9156 (pt0) REVERT: A 224 ASN cc_start: 0.9365 (p0) cc_final: 0.8833 (p0) REVERT: B 100 MET cc_start: 0.9155 (mpp) cc_final: 0.8934 (mpp) REVERT: B 224 ASN cc_start: 0.9298 (p0) cc_final: 0.8726 (p0) REVERT: C 100 MET cc_start: 0.9306 (mpp) cc_final: 0.9042 (mpp) REVERT: C 224 ASN cc_start: 0.9348 (p0) cc_final: 0.8787 (p0) REVERT: D 66 TYR cc_start: 0.8846 (t80) cc_final: 0.8615 (t80) REVERT: D 100 MET cc_start: 0.9146 (mpp) cc_final: 0.8935 (mpp) REVERT: D 224 ASN cc_start: 0.9307 (p0) cc_final: 0.8772 (p0) REVERT: F 100 MET cc_start: 0.9263 (mpp) cc_final: 0.8983 (mpp) REVERT: F 166 GLU cc_start: 0.9378 (mt-10) cc_final: 0.9160 (pt0) REVERT: F 224 ASN cc_start: 0.9358 (p0) cc_final: 0.8805 (p0) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.1249 time to fit residues: 54.7751 Evaluate side-chains 249 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 63 ASN E 173 GLN A 63 ASN B 63 ASN C 63 ASN D 63 ASN D 173 GLN F 63 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.062179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.050069 restraints weight = 54858.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.051077 restraints weight = 43315.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.051882 restraints weight = 35823.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.052539 restraints weight = 30824.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.053068 restraints weight = 27158.734| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9522 Z= 0.158 Angle : 0.830 9.706 12936 Z= 0.413 Chirality : 0.046 0.215 1476 Planarity : 0.005 0.043 1548 Dihedral : 4.461 13.983 1218 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.76 % Allowed : 11.86 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.24), residues: 1110 helix: 0.39 (0.17), residues: 870 sheet: 0.63 (0.65), residues: 60 loop : -2.14 (0.38), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 76 TYR 0.019 0.002 TYR B 66 PHE 0.045 0.002 PHE E 212 TRP 0.016 0.002 TRP C 174 HIS 0.002 0.001 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9504) covalent geometry : angle 0.83041 (12900) SS BOND : bond 0.00128 ( 18) SS BOND : angle 0.75530 ( 36) hydrogen bonds : bond 0.04880 ( 684) hydrogen bonds : angle 4.87803 ( 2034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 310 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 202 ARG cc_start: 0.8512 (tpt170) cc_final: 0.8132 (mtp180) REVERT: A 74 HIS cc_start: 0.9561 (m-70) cc_final: 0.9359 (m-70) REVERT: A 102 LYS cc_start: 0.9418 (pttm) cc_final: 0.8960 (pttm) REVERT: A 104 GLU cc_start: 0.8393 (tp30) cc_final: 0.8116 (tm-30) REVERT: A 105 LYS cc_start: 0.6524 (mmmt) cc_final: 0.5794 (mmmt) REVERT: A 155 TYR cc_start: 0.9312 (t80) cc_final: 0.9050 (t80) REVERT: A 166 GLU cc_start: 0.9404 (mt-10) cc_final: 0.9158 (pt0) REVERT: A 206 LYS cc_start: 0.9305 (ptpt) cc_final: 0.8912 (mttp) REVERT: A 209 PHE cc_start: 0.9739 (m-10) cc_final: 0.9448 (m-80) REVERT: A 224 ASN cc_start: 0.9323 (p0) cc_final: 0.8970 (p0) REVERT: B 74 HIS cc_start: 0.9500 (m-70) cc_final: 0.9269 (m-70) REVERT: B 102 LYS cc_start: 0.9389 (pttm) cc_final: 0.8881 (ptpp) REVERT: B 173 GLN cc_start: 0.9536 (tp-100) cc_final: 0.9304 (tp-100) REVERT: B 206 LYS cc_start: 0.9301 (ptpp) cc_final: 0.9008 (mttp) REVERT: B 209 PHE cc_start: 0.9783 (m-10) cc_final: 0.9481 (m-80) REVERT: C 102 LYS cc_start: 0.9399 (pttm) cc_final: 0.8580 (pttm) REVERT: C 166 GLU cc_start: 0.9034 (pt0) cc_final: 0.8831 (pt0) REVERT: C 206 LYS cc_start: 0.9321 (ptpp) cc_final: 0.9011 (mttp) REVERT: C 209 PHE cc_start: 0.9763 (m-10) cc_final: 0.9468 (m-80) REVERT: D 74 HIS cc_start: 0.9523 (m-70) cc_final: 0.9293 (m-70) REVERT: D 102 LYS cc_start: 0.9384 (pttm) cc_final: 0.8887 (ptpp) REVERT: D 206 LYS cc_start: 0.9306 (ptpp) cc_final: 0.8995 (mttp) REVERT: D 209 PHE cc_start: 0.9772 (m-10) cc_final: 0.9463 (m-80) REVERT: F 74 HIS cc_start: 0.9552 (m-70) cc_final: 0.9029 (m-70) REVERT: F 102 LYS cc_start: 0.9433 (pttm) cc_final: 0.8645 (pttm) REVERT: F 155 TYR cc_start: 0.9322 (t80) cc_final: 0.9043 (t80) REVERT: F 166 GLU cc_start: 0.9411 (mt-10) cc_final: 0.9149 (pt0) REVERT: F 206 LYS cc_start: 0.9281 (ptpt) cc_final: 0.9003 (mttp) REVERT: F 209 PHE cc_start: 0.9744 (m-10) cc_final: 0.9498 (m-80) REVERT: F 224 ASN cc_start: 0.9305 (p0) cc_final: 0.8954 (p0) outliers start: 18 outliers final: 6 residues processed: 322 average time/residue: 0.1243 time to fit residues: 51.7899 Evaluate side-chains 275 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 269 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 chunk 105 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 63 ASN E 173 GLN A 63 ASN A 95 HIS B 63 ASN B 95 HIS C 63 ASN C 95 HIS D 63 ASN D 95 HIS F 63 ASN F 95 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.058549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.046895 restraints weight = 57005.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.047967 restraints weight = 43780.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.048821 restraints weight = 35432.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.049505 restraints weight = 29820.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.050051 restraints weight = 25837.289| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9522 Z= 0.178 Angle : 0.789 10.002 12936 Z= 0.405 Chirality : 0.046 0.280 1476 Planarity : 0.004 0.035 1548 Dihedral : 4.339 17.645 1218 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.86 % Allowed : 15.69 % Favored : 82.45 % 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: 0.45 (0.24), residues: 1110 helix: 0.76 (0.17), residues: 834 sheet: 1.01 (0.63), residues: 60 loop : -1.45 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 202 TYR 0.015 0.002 TYR C 155 PHE 0.040 0.002 PHE F 212 TRP 0.049 0.002 TRP F 78 HIS 0.004 0.001 HIS C 74 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9504) covalent geometry : angle 0.78838 (12900) SS BOND : bond 0.00209 ( 18) SS BOND : angle 0.90205 ( 36) hydrogen bonds : bond 0.04789 ( 684) hydrogen bonds : angle 4.80322 ( 2034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 266 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 HIS cc_start: 0.9523 (m-70) cc_final: 0.9311 (m-70) REVERT: E 173 GLN cc_start: 0.9602 (tp40) cc_final: 0.9390 (tp-100) REVERT: A 23 LYS cc_start: 0.9084 (tptp) cc_final: 0.8875 (tptp) REVERT: A 74 HIS cc_start: 0.9615 (m-70) cc_final: 0.9325 (m-70) REVERT: A 166 GLU cc_start: 0.9415 (mt-10) cc_final: 0.9110 (mt-10) REVERT: A 206 LYS cc_start: 0.9270 (ptpt) cc_final: 0.8825 (mttt) REVERT: A 209 PHE cc_start: 0.9763 (m-10) cc_final: 0.9439 (m-80) REVERT: A 224 ASN cc_start: 0.9282 (p0) cc_final: 0.9033 (p0) REVERT: B 74 HIS cc_start: 0.9588 (m-70) cc_final: 0.9290 (m-70) REVERT: B 166 GLU cc_start: 0.8980 (pt0) cc_final: 0.8773 (pt0) REVERT: B 173 GLN cc_start: 0.9582 (tp-100) cc_final: 0.9347 (tp-100) REVERT: B 206 LYS cc_start: 0.9312 (ptpp) cc_final: 0.8969 (mttp) REVERT: B 209 PHE cc_start: 0.9733 (m-10) cc_final: 0.9403 (m-80) REVERT: C 81 GLN cc_start: 0.9716 (tt0) cc_final: 0.9296 (mt0) REVERT: C 173 GLN cc_start: 0.9605 (tp-100) cc_final: 0.9399 (tp-100) REVERT: C 206 LYS cc_start: 0.9311 (ptpp) cc_final: 0.9056 (mttp) REVERT: C 209 PHE cc_start: 0.9764 (m-10) cc_final: 0.9469 (m-80) REVERT: D 74 HIS cc_start: 0.9590 (m-70) cc_final: 0.9291 (m-70) REVERT: D 166 GLU cc_start: 0.8948 (pt0) cc_final: 0.8746 (pt0) REVERT: D 206 LYS cc_start: 0.9286 (ptpp) cc_final: 0.9024 (mttp) REVERT: D 209 PHE cc_start: 0.9730 (m-10) cc_final: 0.9421 (m-80) REVERT: F 23 LYS cc_start: 0.9075 (tptp) cc_final: 0.8866 (tptp) REVERT: F 74 HIS cc_start: 0.9551 (m-70) cc_final: 0.9212 (m-70) REVERT: F 166 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9125 (mt-10) REVERT: F 206 LYS cc_start: 0.9363 (ptpt) cc_final: 0.9004 (mttp) REVERT: F 209 PHE cc_start: 0.9773 (m-10) cc_final: 0.9459 (m-80) REVERT: F 224 ASN cc_start: 0.9286 (p0) cc_final: 0.9048 (p0) outliers start: 19 outliers final: 10 residues processed: 277 average time/residue: 0.1068 time to fit residues: 39.7940 Evaluate side-chains 260 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 250 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN C 173 GLN D 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.059870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.047843 restraints weight = 57818.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.049050 restraints weight = 43286.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.049965 restraints weight = 34336.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.050684 restraints weight = 28546.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.051234 restraints weight = 24561.613| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9522 Z= 0.161 Angle : 0.836 12.185 12936 Z= 0.423 Chirality : 0.045 0.151 1476 Planarity : 0.004 0.047 1548 Dihedral : 4.271 16.773 1218 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.06 % Allowed : 17.16 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.24), residues: 1110 helix: 0.89 (0.17), residues: 834 sheet: 0.96 (0.61), residues: 60 loop : -1.36 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 202 TYR 0.024 0.002 TYR D 155 PHE 0.045 0.002 PHE F 212 TRP 0.046 0.001 TRP F 78 HIS 0.002 0.001 HIS C 74 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9504) covalent geometry : angle 0.83635 (12900) SS BOND : bond 0.00178 ( 18) SS BOND : angle 0.85903 ( 36) hydrogen bonds : bond 0.04795 ( 684) hydrogen bonds : angle 4.95943 ( 2034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 290 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 HIS cc_start: 0.9473 (m-70) cc_final: 0.9242 (m-70) REVERT: E 92 TYR cc_start: 0.9069 (t80) cc_final: 0.8738 (t80) REVERT: E 162 LYS cc_start: 0.9543 (ptpp) cc_final: 0.9332 (ptpp) REVERT: E 206 LYS cc_start: 0.9295 (mttt) cc_final: 0.8858 (mtpt) REVERT: E 209 PHE cc_start: 0.9678 (m-10) cc_final: 0.9318 (m-80) REVERT: A 23 LYS cc_start: 0.9101 (tptp) cc_final: 0.8853 (tptp) REVERT: A 74 HIS cc_start: 0.9518 (m-70) cc_final: 0.9208 (m-70) REVERT: A 92 TYR cc_start: 0.8816 (t80) cc_final: 0.8451 (t80) REVERT: A 166 GLU cc_start: 0.9359 (mt-10) cc_final: 0.9095 (pt0) REVERT: A 202 ARG cc_start: 0.8751 (mtm180) cc_final: 0.8301 (mtm180) REVERT: A 206 LYS cc_start: 0.9238 (ptpt) cc_final: 0.8781 (mttt) REVERT: A 209 PHE cc_start: 0.9715 (m-10) cc_final: 0.9402 (m-80) REVERT: A 224 ASN cc_start: 0.9240 (p0) cc_final: 0.8773 (p0) REVERT: B 74 HIS cc_start: 0.9468 (m-70) cc_final: 0.9173 (m-70) REVERT: B 92 TYR cc_start: 0.9092 (t80) cc_final: 0.8814 (t80) REVERT: B 101 ARG cc_start: 0.9099 (ttp80) cc_final: 0.8781 (ttp80) REVERT: B 102 LYS cc_start: 0.9112 (pttm) cc_final: 0.8755 (pttm) REVERT: B 173 GLN cc_start: 0.9573 (tp-100) cc_final: 0.9361 (tp-100) REVERT: B 206 LYS cc_start: 0.9272 (ptpp) cc_final: 0.9048 (mttp) REVERT: B 209 PHE cc_start: 0.9659 (m-10) cc_final: 0.9343 (m-80) REVERT: C 42 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8203 (mt-10) REVERT: C 92 TYR cc_start: 0.9092 (t80) cc_final: 0.8799 (t80) REVERT: C 206 LYS cc_start: 0.9282 (ptpp) cc_final: 0.9058 (mttp) REVERT: C 209 PHE cc_start: 0.9715 (m-10) cc_final: 0.9428 (m-80) REVERT: D 74 HIS cc_start: 0.9466 (m-70) cc_final: 0.9174 (m-70) REVERT: D 101 ARG cc_start: 0.9082 (ttp80) cc_final: 0.8770 (ttp80) REVERT: D 102 LYS cc_start: 0.9131 (pttm) cc_final: 0.8771 (pttm) REVERT: D 206 LYS cc_start: 0.9295 (ptpp) cc_final: 0.9034 (mttp) REVERT: D 209 PHE cc_start: 0.9678 (m-10) cc_final: 0.9339 (m-80) REVERT: D 227 GLU cc_start: 0.9663 (mm-30) cc_final: 0.9338 (mm-30) REVERT: F 23 LYS cc_start: 0.9097 (tptp) cc_final: 0.8854 (tptp) REVERT: F 74 HIS cc_start: 0.9507 (m-70) cc_final: 0.9305 (m-70) REVERT: F 166 GLU cc_start: 0.9374 (mt-10) cc_final: 0.9110 (pt0) REVERT: F 202 ARG cc_start: 0.8734 (mtm180) cc_final: 0.8311 (mtm180) REVERT: F 206 LYS cc_start: 0.9273 (ptpt) cc_final: 0.8891 (mttp) REVERT: F 209 PHE cc_start: 0.9708 (m-10) cc_final: 0.9397 (m-80) REVERT: F 224 ASN cc_start: 0.9246 (p0) cc_final: 0.8838 (p0) outliers start: 21 outliers final: 8 residues processed: 300 average time/residue: 0.1155 time to fit residues: 45.6148 Evaluate side-chains 273 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 265 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 50 optimal weight: 0.0980 chunk 58 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 ASN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN D 63 ASN F 15 GLN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.057363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.046000 restraints weight = 60175.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.047201 restraints weight = 44093.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.047984 restraints weight = 34041.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.048608 restraints weight = 28246.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.049076 restraints weight = 24324.727| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9522 Z= 0.203 Angle : 0.821 11.847 12936 Z= 0.430 Chirality : 0.046 0.264 1476 Planarity : 0.004 0.027 1548 Dihedral : 4.354 16.255 1218 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 22.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.96 % Allowed : 21.67 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.24), residues: 1110 helix: 0.95 (0.17), residues: 870 sheet: 0.89 (0.59), residues: 60 loop : -1.72 (0.38), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 202 TYR 0.016 0.002 TYR D 155 PHE 0.039 0.002 PHE B 212 TRP 0.051 0.001 TRP F 78 HIS 0.006 0.001 HIS C 74 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 9504) covalent geometry : angle 0.82048 (12900) SS BOND : bond 0.00259 ( 18) SS BOND : angle 0.87968 ( 36) hydrogen bonds : bond 0.04881 ( 684) hydrogen bonds : angle 5.12298 ( 2034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 282 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 17 TYR cc_start: 0.8527 (m-10) cc_final: 0.8009 (m-10) REVERT: E 42 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8410 (mt-10) REVERT: E 74 HIS cc_start: 0.9583 (m-70) cc_final: 0.9281 (m90) REVERT: E 81 GLN cc_start: 0.9684 (tt0) cc_final: 0.9340 (mt0) REVERT: E 92 TYR cc_start: 0.9203 (t80) cc_final: 0.8945 (t80) REVERT: E 102 LYS cc_start: 0.9095 (pttm) cc_final: 0.8879 (pttm) REVERT: E 173 GLN cc_start: 0.9635 (tp-100) cc_final: 0.9399 (tp-100) REVERT: E 227 GLU cc_start: 0.9766 (mm-30) cc_final: 0.9475 (mm-30) REVERT: A 17 TYR cc_start: 0.8527 (m-10) cc_final: 0.8063 (m-10) REVERT: A 33 ARG cc_start: 0.9277 (mtm110) cc_final: 0.9070 (mtm110) REVERT: A 42 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8343 (mt-10) REVERT: A 74 HIS cc_start: 0.9608 (m-70) cc_final: 0.9205 (m-70) REVERT: A 92 TYR cc_start: 0.9011 (t80) cc_final: 0.8808 (t80) REVERT: A 179 PHE cc_start: 0.8252 (m-80) cc_final: 0.7624 (m-80) REVERT: A 190 ASP cc_start: 0.9058 (t0) cc_final: 0.8796 (p0) REVERT: A 202 ARG cc_start: 0.8760 (mtm180) cc_final: 0.8166 (mtm180) REVERT: A 206 LYS cc_start: 0.9298 (ptpt) cc_final: 0.9026 (mttp) REVERT: A 209 PHE cc_start: 0.9732 (m-10) cc_final: 0.9384 (m-80) REVERT: A 227 GLU cc_start: 0.9774 (mm-30) cc_final: 0.9460 (mm-30) REVERT: B 17 TYR cc_start: 0.8657 (m-80) cc_final: 0.8031 (m-10) REVERT: B 42 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8442 (mt-10) REVERT: B 74 HIS cc_start: 0.9566 (m-70) cc_final: 0.9179 (m-70) REVERT: B 92 TYR cc_start: 0.9263 (t80) cc_final: 0.9038 (t80) REVERT: B 173 GLN cc_start: 0.9617 (tp-100) cc_final: 0.9403 (tp-100) REVERT: B 190 ASP cc_start: 0.8956 (t0) cc_final: 0.8683 (p0) REVERT: B 206 LYS cc_start: 0.9380 (ptpp) cc_final: 0.9154 (mttp) REVERT: B 209 PHE cc_start: 0.9720 (m-10) cc_final: 0.9349 (m-80) REVERT: C 17 TYR cc_start: 0.8531 (m-10) cc_final: 0.8019 (m-10) REVERT: C 42 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8385 (mt-10) REVERT: C 81 GLN cc_start: 0.9728 (tt0) cc_final: 0.9262 (mt0) REVERT: C 92 TYR cc_start: 0.9230 (t80) cc_final: 0.8991 (t80) REVERT: C 160 LEU cc_start: 0.9911 (mt) cc_final: 0.9680 (pp) REVERT: C 173 GLN cc_start: 0.9625 (tp-100) cc_final: 0.9385 (tp-100) REVERT: C 202 ARG cc_start: 0.8829 (mtm180) cc_final: 0.8478 (mtm180) REVERT: C 206 LYS cc_start: 0.9394 (ptpp) cc_final: 0.9190 (mttp) REVERT: C 209 PHE cc_start: 0.9723 (m-10) cc_final: 0.9419 (m-80) REVERT: C 227 GLU cc_start: 0.9769 (mm-30) cc_final: 0.9472 (mm-30) REVERT: D 17 TYR cc_start: 0.8558 (m-10) cc_final: 0.8096 (m-10) REVERT: D 42 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8427 (mt-10) REVERT: D 74 HIS cc_start: 0.9544 (m-70) cc_final: 0.9156 (m-70) REVERT: D 92 TYR cc_start: 0.9281 (t80) cc_final: 0.9063 (t80) REVERT: D 190 ASP cc_start: 0.8972 (t0) cc_final: 0.8702 (p0) REVERT: D 202 ARG cc_start: 0.8786 (mtm180) cc_final: 0.8489 (mtm180) REVERT: D 209 PHE cc_start: 0.9728 (m-10) cc_final: 0.9363 (m-80) REVERT: D 227 GLU cc_start: 0.9730 (mm-30) cc_final: 0.9401 (mm-30) REVERT: F 17 TYR cc_start: 0.8544 (m-10) cc_final: 0.8115 (m-10) REVERT: F 42 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8436 (mt-10) REVERT: F 74 HIS cc_start: 0.9573 (m-70) cc_final: 0.9351 (m-70) REVERT: F 92 TYR cc_start: 0.9024 (t80) cc_final: 0.8781 (t80) REVERT: F 166 GLU cc_start: 0.9405 (mt-10) cc_final: 0.9180 (mt-10) REVERT: F 179 PHE cc_start: 0.8301 (m-80) cc_final: 0.7706 (m-80) REVERT: F 190 ASP cc_start: 0.9051 (t0) cc_final: 0.8796 (p0) REVERT: F 206 LYS cc_start: 0.9343 (ptpt) cc_final: 0.9061 (mttp) REVERT: F 209 PHE cc_start: 0.9678 (m-10) cc_final: 0.9375 (m-80) REVERT: F 213 MET cc_start: 0.9454 (ppp) cc_final: 0.9172 (ppp) REVERT: F 214 LEU cc_start: 0.9729 (OUTLIER) cc_final: 0.9309 (mm) REVERT: F 227 GLU cc_start: 0.9791 (mm-30) cc_final: 0.9469 (mm-30) outliers start: 20 outliers final: 14 residues processed: 294 average time/residue: 0.1106 time to fit residues: 43.3062 Evaluate side-chains 270 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 255 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 214 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 75 optimal weight: 6.9990 chunk 62 optimal weight: 0.1980 chunk 89 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 173 GLN A 15 GLN B 15 GLN ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN D 63 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.056899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.045950 restraints weight = 61607.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.046983 restraints weight = 45392.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.047779 restraints weight = 35729.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.048387 restraints weight = 29666.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.048825 restraints weight = 25540.050| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9522 Z= 0.175 Angle : 0.844 12.398 12936 Z= 0.438 Chirality : 0.045 0.194 1476 Planarity : 0.004 0.025 1548 Dihedral : 4.294 15.380 1218 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.47 % Allowed : 27.25 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.24), residues: 1110 helix: 0.92 (0.17), residues: 870 sheet: 0.97 (0.57), residues: 60 loop : -1.64 (0.39), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 101 TYR 0.011 0.001 TYR D 155 PHE 0.045 0.002 PHE C 212 TRP 0.045 0.002 TRP E 78 HIS 0.010 0.001 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9504) covalent geometry : angle 0.84354 (12900) SS BOND : bond 0.00205 ( 18) SS BOND : angle 0.86904 ( 36) hydrogen bonds : bond 0.04807 ( 684) hydrogen bonds : angle 5.12453 ( 2034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 273 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 17 TYR cc_start: 0.8535 (m-10) cc_final: 0.8068 (m-10) REVERT: E 42 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8423 (mt-10) REVERT: E 74 HIS cc_start: 0.9582 (m-70) cc_final: 0.9161 (m-70) REVERT: E 77 PHE cc_start: 0.9639 (t80) cc_final: 0.9258 (t80) REVERT: E 78 TRP cc_start: 0.9069 (m-90) cc_final: 0.8673 (m-90) REVERT: E 81 GLN cc_start: 0.9672 (tt0) cc_final: 0.9424 (mt0) REVERT: E 92 TYR cc_start: 0.9256 (t80) cc_final: 0.8980 (t80) REVERT: E 202 ARG cc_start: 0.9211 (mtm180) cc_final: 0.8691 (ptm160) REVERT: E 209 PHE cc_start: 0.9690 (m-10) cc_final: 0.9277 (m-80) REVERT: E 214 LEU cc_start: 0.9737 (OUTLIER) cc_final: 0.9515 (mt) REVERT: E 227 GLU cc_start: 0.9773 (mm-30) cc_final: 0.9469 (mm-30) REVERT: A 17 TYR cc_start: 0.8599 (m-10) cc_final: 0.8174 (m-10) REVERT: A 37 LEU cc_start: 0.9480 (pp) cc_final: 0.9072 (pp) REVERT: A 42 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8412 (mt-10) REVERT: A 74 HIS cc_start: 0.9610 (m-70) cc_final: 0.9199 (m-70) REVERT: A 92 TYR cc_start: 0.9143 (t80) cc_final: 0.8815 (t80) REVERT: A 100 MET cc_start: 0.9600 (tpt) cc_final: 0.9395 (mmm) REVERT: A 161 PHE cc_start: 0.9474 (m-80) cc_final: 0.9077 (m-80) REVERT: A 202 ARG cc_start: 0.8741 (mtm180) cc_final: 0.8315 (mtm180) REVERT: A 206 LYS cc_start: 0.9316 (ptpt) cc_final: 0.9086 (mttp) REVERT: A 209 PHE cc_start: 0.9742 (m-10) cc_final: 0.9381 (m-80) REVERT: A 227 GLU cc_start: 0.9785 (mm-30) cc_final: 0.9464 (mm-30) REVERT: B 17 TYR cc_start: 0.8679 (m-80) cc_final: 0.8092 (m-10) REVERT: B 42 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8462 (mt-10) REVERT: B 74 HIS cc_start: 0.9543 (m-70) cc_final: 0.9172 (m-70) REVERT: B 92 TYR cc_start: 0.9286 (t80) cc_final: 0.9053 (t80) REVERT: B 173 GLN cc_start: 0.9615 (tp-100) cc_final: 0.9397 (tp-100) REVERT: B 209 PHE cc_start: 0.9653 (m-10) cc_final: 0.9268 (m-80) REVERT: C 17 TYR cc_start: 0.8526 (m-10) cc_final: 0.8066 (m-10) REVERT: C 42 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8390 (mt-10) REVERT: C 81 GLN cc_start: 0.9724 (tt0) cc_final: 0.9363 (mt0) REVERT: C 202 ARG cc_start: 0.8784 (mtm180) cc_final: 0.8508 (mtm180) REVERT: C 209 PHE cc_start: 0.9733 (m-10) cc_final: 0.9422 (m-80) REVERT: C 227 GLU cc_start: 0.9777 (mm-30) cc_final: 0.9465 (mm-30) REVERT: D 17 TYR cc_start: 0.8558 (m-10) cc_final: 0.8141 (m-10) REVERT: D 33 ARG cc_start: 0.9262 (mtm110) cc_final: 0.9061 (mtm110) REVERT: D 42 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8418 (mt-10) REVERT: D 74 HIS cc_start: 0.9541 (m-70) cc_final: 0.9161 (m-70) REVERT: D 202 ARG cc_start: 0.8638 (mtm180) cc_final: 0.8414 (mtm180) REVERT: D 209 PHE cc_start: 0.9660 (m-10) cc_final: 0.9294 (m-80) REVERT: F 17 TYR cc_start: 0.8618 (m-10) cc_final: 0.8215 (m-10) REVERT: F 42 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8445 (mt-10) REVERT: F 74 HIS cc_start: 0.9625 (m-70) cc_final: 0.9349 (m-70) REVERT: F 92 TYR cc_start: 0.9055 (t80) cc_final: 0.8747 (t80) REVERT: F 206 LYS cc_start: 0.9315 (ptpt) cc_final: 0.9063 (mttp) REVERT: F 209 PHE cc_start: 0.9675 (m-10) cc_final: 0.9347 (m-80) REVERT: F 214 LEU cc_start: 0.9737 (OUTLIER) cc_final: 0.9389 (mm) REVERT: F 227 GLU cc_start: 0.9796 (mm-30) cc_final: 0.9553 (mm-30) outliers start: 15 outliers final: 10 residues processed: 280 average time/residue: 0.1048 time to fit residues: 39.4086 Evaluate side-chains 266 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 254 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 214 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 0.0770 chunk 78 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** F 63 ASN ** 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 = 0.3240 r_free = 0.3240 target = 0.054727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.043733 restraints weight = 60872.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.044701 restraints weight = 46110.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.045452 restraints weight = 36947.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.046012 restraints weight = 30957.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.046472 restraints weight = 26907.896| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9522 Z= 0.167 Angle : 0.887 13.210 12936 Z= 0.462 Chirality : 0.046 0.216 1476 Planarity : 0.004 0.023 1548 Dihedral : 4.238 17.664 1218 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.86 % Allowed : 29.31 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.24), residues: 1110 helix: 1.18 (0.18), residues: 828 sheet: 1.08 (0.58), residues: 60 loop : -1.89 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 76 TYR 0.013 0.001 TYR D 155 PHE 0.028 0.002 PHE E 212 TRP 0.038 0.002 TRP C 78 HIS 0.002 0.001 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9504) covalent geometry : angle 0.88760 (12900) SS BOND : bond 0.00167 ( 18) SS BOND : angle 0.77459 ( 36) hydrogen bonds : bond 0.04771 ( 684) hydrogen bonds : angle 5.14097 ( 2034) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 285 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 17 TYR cc_start: 0.8427 (m-10) cc_final: 0.7998 (m-10) REVERT: E 42 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8419 (mt-10) REVERT: E 74 HIS cc_start: 0.9485 (m-70) cc_final: 0.9014 (m-70) REVERT: E 75 VAL cc_start: 0.9390 (OUTLIER) cc_final: 0.9037 (m) REVERT: E 77 PHE cc_start: 0.9583 (t80) cc_final: 0.9162 (t80) REVERT: E 78 TRP cc_start: 0.9196 (m-10) cc_final: 0.8718 (m-90) REVERT: E 81 GLN cc_start: 0.9668 (tt0) cc_final: 0.9433 (mt0) REVERT: E 162 LYS cc_start: 0.9585 (ptpp) cc_final: 0.9378 (ptpp) REVERT: E 173 GLN cc_start: 0.9577 (tp-100) cc_final: 0.9376 (tp-100) REVERT: E 190 ASP cc_start: 0.8969 (t0) cc_final: 0.8488 (p0) REVERT: E 202 ARG cc_start: 0.9133 (mtm180) cc_final: 0.8849 (ptm160) REVERT: E 209 PHE cc_start: 0.9657 (m-10) cc_final: 0.9231 (m-80) REVERT: E 214 LEU cc_start: 0.9697 (OUTLIER) cc_final: 0.9483 (mt) REVERT: E 227 GLU cc_start: 0.9767 (mm-30) cc_final: 0.9452 (mm-30) REVERT: A 17 TYR cc_start: 0.8525 (m-10) cc_final: 0.8136 (m-10) REVERT: A 33 ARG cc_start: 0.9291 (mtm110) cc_final: 0.9044 (mtm110) REVERT: A 37 LEU cc_start: 0.9491 (pp) cc_final: 0.9048 (pp) REVERT: A 42 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8362 (mt-10) REVERT: A 74 HIS cc_start: 0.9433 (m-70) cc_final: 0.9045 (m-70) REVERT: A 92 TYR cc_start: 0.9049 (t80) cc_final: 0.8783 (t80) REVERT: A 202 ARG cc_start: 0.8758 (mtm180) cc_final: 0.8347 (mtm180) REVERT: A 206 LYS cc_start: 0.9288 (ptpt) cc_final: 0.9046 (mttp) REVERT: A 209 PHE cc_start: 0.9708 (m-10) cc_final: 0.9333 (m-80) REVERT: A 227 GLU cc_start: 0.9787 (mm-30) cc_final: 0.9504 (mm-30) REVERT: B 17 TYR cc_start: 0.8593 (m-80) cc_final: 0.8026 (m-10) REVERT: B 33 ARG cc_start: 0.9260 (mtm110) cc_final: 0.9017 (mtm110) REVERT: B 37 LEU cc_start: 0.9486 (pp) cc_final: 0.9063 (pp) REVERT: B 42 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8433 (mt-10) REVERT: B 74 HIS cc_start: 0.9368 (m-70) cc_final: 0.8985 (m-70) REVERT: B 173 GLN cc_start: 0.9565 (tp-100) cc_final: 0.9352 (tp-100) REVERT: B 190 ASP cc_start: 0.8881 (t0) cc_final: 0.8671 (p0) REVERT: B 209 PHE cc_start: 0.9584 (m-10) cc_final: 0.9182 (m-80) REVERT: B 227 GLU cc_start: 0.9744 (mm-30) cc_final: 0.9402 (mm-30) REVERT: C 17 TYR cc_start: 0.8406 (m-10) cc_final: 0.7968 (m-10) REVERT: C 42 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8351 (mt-10) REVERT: C 77 PHE cc_start: 0.9574 (t80) cc_final: 0.9137 (t80) REVERT: C 78 TRP cc_start: 0.8768 (m-90) cc_final: 0.8352 (m-90) REVERT: C 81 GLN cc_start: 0.9678 (tt0) cc_final: 0.9467 (mt0) REVERT: C 190 ASP cc_start: 0.8984 (t0) cc_final: 0.8497 (p0) REVERT: C 209 PHE cc_start: 0.9669 (m-10) cc_final: 0.9354 (m-80) REVERT: C 227 GLU cc_start: 0.9762 (mm-30) cc_final: 0.9443 (mm-30) REVERT: D 17 TYR cc_start: 0.8450 (m-10) cc_final: 0.8083 (m-10) REVERT: D 33 ARG cc_start: 0.9252 (mtm110) cc_final: 0.9007 (mtm110) REVERT: D 37 LEU cc_start: 0.9476 (pp) cc_final: 0.9043 (pp) REVERT: D 42 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8356 (mt-10) REVERT: D 74 HIS cc_start: 0.9332 (m-70) cc_final: 0.8951 (m-70) REVERT: D 202 ARG cc_start: 0.8606 (mtm180) cc_final: 0.8198 (mtm180) REVERT: D 209 PHE cc_start: 0.9611 (m-10) cc_final: 0.9205 (m-80) REVERT: D 227 GLU cc_start: 0.9723 (mm-30) cc_final: 0.9376 (mm-30) REVERT: F 17 TYR cc_start: 0.8538 (m-10) cc_final: 0.8156 (m-10) REVERT: F 42 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8394 (mt-10) REVERT: F 74 HIS cc_start: 0.9527 (m-70) cc_final: 0.9232 (m-70) REVERT: F 92 TYR cc_start: 0.9012 (t80) cc_final: 0.8795 (t80) REVERT: F 161 PHE cc_start: 0.9480 (m-80) cc_final: 0.9047 (m-80) REVERT: F 162 LYS cc_start: 0.9559 (ptpp) cc_final: 0.9318 (ptpp) REVERT: F 206 LYS cc_start: 0.9291 (ptpt) cc_final: 0.9022 (mttp) REVERT: F 209 PHE cc_start: 0.9619 (m-10) cc_final: 0.9267 (m-80) REVERT: F 214 LEU cc_start: 0.9724 (OUTLIER) cc_final: 0.9451 (mm) REVERT: F 227 GLU cc_start: 0.9780 (mm-30) cc_final: 0.9535 (mm-30) outliers start: 19 outliers final: 3 residues processed: 297 average time/residue: 0.1059 time to fit residues: 42.3642 Evaluate side-chains 266 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 260 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain F residue 214 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 60 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.053353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.043089 restraints weight = 63416.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.044061 restraints weight = 45494.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.044714 restraints weight = 35553.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.045292 restraints weight = 29665.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.045687 restraints weight = 25590.845| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9522 Z= 0.216 Angle : 0.918 11.524 12936 Z= 0.489 Chirality : 0.046 0.177 1476 Planarity : 0.005 0.033 1548 Dihedral : 4.369 20.691 1218 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 25.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.18 % Allowed : 31.76 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.25), residues: 1110 helix: 1.23 (0.18), residues: 828 sheet: 1.06 (0.59), residues: 60 loop : -1.92 (0.35), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 202 TYR 0.015 0.001 TYR B 98 PHE 0.031 0.002 PHE A 179 TRP 0.029 0.002 TRP C 78 HIS 0.003 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 9504) covalent geometry : angle 0.91834 (12900) SS BOND : bond 0.00239 ( 18) SS BOND : angle 0.74973 ( 36) hydrogen bonds : bond 0.04956 ( 684) hydrogen bonds : angle 5.42725 ( 2034) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 281 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 17 TYR cc_start: 0.8557 (m-10) cc_final: 0.8098 (m-10) REVERT: E 42 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8584 (mt-10) REVERT: E 74 HIS cc_start: 0.9527 (m-70) cc_final: 0.9062 (m-70) REVERT: E 75 VAL cc_start: 0.9437 (OUTLIER) cc_final: 0.8983 (m) REVERT: E 77 PHE cc_start: 0.9611 (t80) cc_final: 0.9152 (t80) REVERT: E 78 TRP cc_start: 0.9351 (m-10) cc_final: 0.8761 (m-90) REVERT: E 81 GLN cc_start: 0.9653 (tt0) cc_final: 0.9401 (mt0) REVERT: E 179 PHE cc_start: 0.8321 (m-80) cc_final: 0.7993 (m-80) REVERT: E 202 ARG cc_start: 0.9234 (mtm180) cc_final: 0.8812 (ptm160) REVERT: E 214 LEU cc_start: 0.9723 (OUTLIER) cc_final: 0.9440 (mm) REVERT: E 227 GLU cc_start: 0.9789 (mm-30) cc_final: 0.9491 (mm-30) REVERT: A 17 TYR cc_start: 0.8639 (m-10) cc_final: 0.8257 (m-10) REVERT: A 33 ARG cc_start: 0.9316 (mtm110) cc_final: 0.9004 (mtm110) REVERT: A 42 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8472 (mt-10) REVERT: A 92 TYR cc_start: 0.9182 (t80) cc_final: 0.8912 (t80) REVERT: A 202 ARG cc_start: 0.8845 (mtm180) cc_final: 0.8439 (mtm180) REVERT: A 206 LYS cc_start: 0.9382 (ptpt) cc_final: 0.9136 (mttp) REVERT: A 209 PHE cc_start: 0.9749 (m-10) cc_final: 0.9386 (m-80) REVERT: A 227 GLU cc_start: 0.9799 (mm-30) cc_final: 0.9534 (mm-30) REVERT: B 17 TYR cc_start: 0.8667 (m-80) cc_final: 0.8139 (m-10) REVERT: B 33 ARG cc_start: 0.9307 (mtm110) cc_final: 0.9061 (mtm110) REVERT: B 42 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8542 (mt-10) REVERT: B 74 HIS cc_start: 0.9476 (m-70) cc_final: 0.9037 (m-70) REVERT: B 173 GLN cc_start: 0.9614 (tp-100) cc_final: 0.9397 (tp-100) REVERT: B 190 ASP cc_start: 0.8966 (t0) cc_final: 0.8739 (p0) REVERT: B 209 PHE cc_start: 0.9652 (m-10) cc_final: 0.9252 (m-80) REVERT: B 227 GLU cc_start: 0.9779 (mm-30) cc_final: 0.9488 (mm-30) REVERT: C 17 TYR cc_start: 0.8538 (m-10) cc_final: 0.8089 (m-10) REVERT: C 42 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8537 (mt-10) REVERT: C 77 PHE cc_start: 0.9607 (t80) cc_final: 0.9338 (t80) REVERT: C 78 TRP cc_start: 0.9124 (m-90) cc_final: 0.8449 (m-90) REVERT: C 209 PHE cc_start: 0.9698 (m-10) cc_final: 0.9396 (m-80) REVERT: C 227 GLU cc_start: 0.9783 (mm-30) cc_final: 0.9475 (mm-30) REVERT: D 17 TYR cc_start: 0.8539 (m-10) cc_final: 0.8176 (m-10) REVERT: D 42 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8537 (mt-10) REVERT: D 74 HIS cc_start: 0.9468 (m-70) cc_final: 0.9020 (m-70) REVERT: D 206 LYS cc_start: 0.9328 (mttp) cc_final: 0.8943 (mttp) REVERT: D 209 PHE cc_start: 0.9665 (m-10) cc_final: 0.9274 (m-80) REVERT: D 227 GLU cc_start: 0.9753 (mm-30) cc_final: 0.9453 (mm-30) REVERT: F 17 TYR cc_start: 0.8629 (m-10) cc_final: 0.8248 (m-10) REVERT: F 33 ARG cc_start: 0.9320 (mtm110) cc_final: 0.9050 (mtm110) REVERT: F 161 PHE cc_start: 0.9466 (m-80) cc_final: 0.8994 (m-80) REVERT: F 202 ARG cc_start: 0.8838 (mtm180) cc_final: 0.8558 (ptt90) REVERT: F 206 LYS cc_start: 0.9375 (ptpt) cc_final: 0.9127 (mttp) REVERT: F 209 PHE cc_start: 0.9680 (m-10) cc_final: 0.9363 (m-80) REVERT: F 227 GLU cc_start: 0.9805 (mm-30) cc_final: 0.9521 (mm-30) outliers start: 12 outliers final: 3 residues processed: 287 average time/residue: 0.1094 time to fit residues: 42.0355 Evaluate side-chains 267 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 262 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain A residue 91 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 104 optimal weight: 0.0050 chunk 66 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** 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 = 0.3223 r_free = 0.3223 target = 0.054063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.043355 restraints weight = 62890.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.044328 restraints weight = 46270.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.045074 restraints weight = 36442.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.045629 restraints weight = 30250.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.046059 restraints weight = 26152.907| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.6479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9522 Z= 0.183 Angle : 1.045 17.917 12936 Z= 0.534 Chirality : 0.048 0.251 1476 Planarity : 0.004 0.037 1548 Dihedral : 4.235 20.559 1218 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.78 % Allowed : 34.71 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.24), residues: 1110 helix: 1.14 (0.18), residues: 828 sheet: 0.98 (0.58), residues: 60 loop : -1.96 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 33 TYR 0.022 0.001 TYR A 230 PHE 0.033 0.002 PHE C 179 TRP 0.041 0.002 TRP A 78 HIS 0.002 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9504) covalent geometry : angle 1.04626 (12900) SS BOND : bond 0.00144 ( 18) SS BOND : angle 0.66823 ( 36) hydrogen bonds : bond 0.05095 ( 684) hydrogen bonds : angle 5.28707 ( 2034) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 289 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 17 TYR cc_start: 0.8535 (m-10) cc_final: 0.8148 (m-10) REVERT: E 42 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8513 (mt-10) REVERT: E 74 HIS cc_start: 0.9441 (m-70) cc_final: 0.9093 (m90) REVERT: E 75 VAL cc_start: 0.9422 (OUTLIER) cc_final: 0.8839 (m) REVERT: E 78 TRP cc_start: 0.9270 (m-10) cc_final: 0.8523 (m-90) REVERT: E 162 LYS cc_start: 0.9577 (ptpp) cc_final: 0.9355 (ptpp) REVERT: E 179 PHE cc_start: 0.8480 (m-80) cc_final: 0.8096 (m-80) REVERT: E 209 PHE cc_start: 0.9638 (m-10) cc_final: 0.9220 (m-80) REVERT: E 214 LEU cc_start: 0.9752 (OUTLIER) cc_final: 0.9424 (mm) REVERT: E 227 GLU cc_start: 0.9789 (mm-30) cc_final: 0.9485 (mm-30) REVERT: A 17 TYR cc_start: 0.8594 (m-10) cc_final: 0.8229 (m-10) REVERT: A 33 ARG cc_start: 0.9325 (mtm110) cc_final: 0.9121 (mtm110) REVERT: A 74 HIS cc_start: 0.9182 (m-70) cc_final: 0.8917 (m-70) REVERT: A 92 TYR cc_start: 0.9139 (t80) cc_final: 0.8928 (t80) REVERT: A 202 ARG cc_start: 0.8836 (mtm180) cc_final: 0.8420 (mtm180) REVERT: A 206 LYS cc_start: 0.9321 (ptpt) cc_final: 0.9088 (mttp) REVERT: A 209 PHE cc_start: 0.9714 (m-10) cc_final: 0.9350 (m-80) REVERT: A 227 GLU cc_start: 0.9801 (mm-30) cc_final: 0.9512 (mm-30) REVERT: B 17 TYR cc_start: 0.8646 (m-80) cc_final: 0.8085 (m-10) REVERT: B 33 ARG cc_start: 0.9329 (mtm110) cc_final: 0.9115 (mtm110) REVERT: B 74 HIS cc_start: 0.9326 (m-70) cc_final: 0.8894 (m-70) REVERT: B 173 GLN cc_start: 0.9579 (tp-100) cc_final: 0.9369 (tp-100) REVERT: B 179 PHE cc_start: 0.8352 (m-80) cc_final: 0.8039 (m-80) REVERT: B 190 ASP cc_start: 0.8933 (t0) cc_final: 0.8729 (p0) REVERT: B 209 PHE cc_start: 0.9621 (m-10) cc_final: 0.9222 (m-80) REVERT: B 227 GLU cc_start: 0.9774 (mm-30) cc_final: 0.9470 (mm-30) REVERT: C 17 TYR cc_start: 0.8526 (m-10) cc_final: 0.8147 (m-10) REVERT: C 42 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8441 (mt-10) REVERT: C 78 TRP cc_start: 0.8940 (m-90) cc_final: 0.8682 (m-90) REVERT: C 206 LYS cc_start: 0.9324 (mttp) cc_final: 0.9000 (mttp) REVERT: C 209 PHE cc_start: 0.9680 (m-10) cc_final: 0.9363 (m-80) REVERT: C 227 GLU cc_start: 0.9791 (mm-30) cc_final: 0.9477 (mm-30) REVERT: D 17 TYR cc_start: 0.8473 (m-10) cc_final: 0.8119 (m-10) REVERT: D 33 ARG cc_start: 0.9341 (mtm110) cc_final: 0.9103 (mtm180) REVERT: D 74 HIS cc_start: 0.9291 (m-70) cc_final: 0.8854 (m-70) REVERT: D 206 LYS cc_start: 0.9327 (mttp) cc_final: 0.8980 (mttp) REVERT: D 209 PHE cc_start: 0.9635 (m-10) cc_final: 0.9263 (m-80) REVERT: D 227 GLU cc_start: 0.9755 (mm-30) cc_final: 0.9420 (mm-30) REVERT: F 17 TYR cc_start: 0.8612 (m-10) cc_final: 0.8255 (m-10) REVERT: F 37 LEU cc_start: 0.9604 (pp) cc_final: 0.9192 (pp) REVERT: F 42 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8502 (mt-10) REVERT: F 206 LYS cc_start: 0.9304 (ptpt) cc_final: 0.9094 (mttp) REVERT: F 209 PHE cc_start: 0.9636 (m-10) cc_final: 0.9292 (m-80) REVERT: F 227 GLU cc_start: 0.9790 (mm-30) cc_final: 0.9501 (mm-30) outliers start: 8 outliers final: 2 residues processed: 295 average time/residue: 0.1102 time to fit residues: 43.3754 Evaluate side-chains 282 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 278 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 68 optimal weight: 0.0020 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.054950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.044427 restraints weight = 61016.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.045423 restraints weight = 44148.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.046154 restraints weight = 34528.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.046713 restraints weight = 28650.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.047137 restraints weight = 24737.815| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.6618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9522 Z= 0.185 Angle : 1.097 18.178 12936 Z= 0.553 Chirality : 0.048 0.202 1476 Planarity : 0.004 0.036 1548 Dihedral : 4.258 20.374 1218 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 25.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.49 % Allowed : 34.51 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.24), residues: 1110 helix: 1.03 (0.18), residues: 828 sheet: 1.06 (0.59), residues: 60 loop : -2.00 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 33 TYR 0.017 0.001 TYR D 230 PHE 0.029 0.002 PHE E 212 TRP 0.042 0.002 TRP A 78 HIS 0.002 0.001 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9504) covalent geometry : angle 1.09818 (12900) SS BOND : bond 0.00160 ( 18) SS BOND : angle 0.63739 ( 36) hydrogen bonds : bond 0.05067 ( 684) hydrogen bonds : angle 5.36580 ( 2034) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 284 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 17 TYR cc_start: 0.8531 (m-10) cc_final: 0.8155 (m-10) REVERT: E 42 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8597 (mt-10) REVERT: E 74 HIS cc_start: 0.9478 (m-70) cc_final: 0.9163 (m90) REVERT: E 75 VAL cc_start: 0.9420 (OUTLIER) cc_final: 0.8855 (m) REVERT: E 77 PHE cc_start: 0.9507 (t80) cc_final: 0.9171 (t80) REVERT: E 78 TRP cc_start: 0.9283 (m-10) cc_final: 0.8476 (m-90) REVERT: E 81 GLN cc_start: 0.9695 (tt0) cc_final: 0.9431 (mt0) REVERT: E 179 PHE cc_start: 0.8448 (m-80) cc_final: 0.8040 (m-80) REVERT: E 190 ASP cc_start: 0.9069 (t0) cc_final: 0.8740 (p0) REVERT: E 202 ARG cc_start: 0.9187 (mtm180) cc_final: 0.8378 (ptm160) REVERT: E 205 GLU cc_start: 0.8879 (pm20) cc_final: 0.8499 (pm20) REVERT: E 209 PHE cc_start: 0.9650 (m-10) cc_final: 0.9056 (m-80) REVERT: E 214 LEU cc_start: 0.9756 (OUTLIER) cc_final: 0.9424 (mm) REVERT: E 227 GLU cc_start: 0.9794 (mm-30) cc_final: 0.9484 (mm-30) REVERT: A 17 TYR cc_start: 0.8595 (m-10) cc_final: 0.8230 (m-10) REVERT: A 33 ARG cc_start: 0.9285 (mtm110) cc_final: 0.9049 (mtm110) REVERT: A 42 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8496 (mt-10) REVERT: A 74 HIS cc_start: 0.9255 (m-70) cc_final: 0.9002 (m-70) REVERT: A 92 TYR cc_start: 0.9254 (t80) cc_final: 0.9027 (t80) REVERT: A 206 LYS cc_start: 0.9339 (ptpt) cc_final: 0.9130 (mttp) REVERT: A 209 PHE cc_start: 0.9754 (m-10) cc_final: 0.9421 (m-80) REVERT: A 227 GLU cc_start: 0.9802 (mm-30) cc_final: 0.9528 (mm-30) REVERT: B 17 TYR cc_start: 0.8657 (m-80) cc_final: 0.8101 (m-10) REVERT: B 33 ARG cc_start: 0.9273 (mtm110) cc_final: 0.9035 (mtm110) REVERT: B 42 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8449 (mt-10) REVERT: B 74 HIS cc_start: 0.9410 (m-70) cc_final: 0.8966 (m-70) REVERT: B 179 PHE cc_start: 0.8243 (m-80) cc_final: 0.7870 (m-80) REVERT: B 209 PHE cc_start: 0.9665 (m-10) cc_final: 0.9267 (m-80) REVERT: B 227 GLU cc_start: 0.9767 (mm-30) cc_final: 0.9477 (mm-30) REVERT: C 17 TYR cc_start: 0.8535 (m-10) cc_final: 0.8163 (m-10) REVERT: C 42 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8472 (mt-10) REVERT: C 190 ASP cc_start: 0.9081 (t0) cc_final: 0.8752 (p0) REVERT: C 206 LYS cc_start: 0.9449 (mttp) cc_final: 0.9042 (mttp) REVERT: C 209 PHE cc_start: 0.9664 (m-10) cc_final: 0.9328 (m-80) REVERT: C 227 GLU cc_start: 0.9797 (mm-30) cc_final: 0.9480 (mm-30) REVERT: D 17 TYR cc_start: 0.8512 (m-10) cc_final: 0.8143 (m-10) REVERT: D 74 HIS cc_start: 0.9343 (m-70) cc_final: 0.8853 (m-70) REVERT: D 206 LYS cc_start: 0.9376 (mttp) cc_final: 0.9021 (mttp) REVERT: D 209 PHE cc_start: 0.9691 (m-10) cc_final: 0.9311 (m-80) REVERT: D 227 GLU cc_start: 0.9757 (mm-30) cc_final: 0.9453 (mm-30) REVERT: F 17 TYR cc_start: 0.8635 (m-10) cc_final: 0.8270 (m-10) REVERT: F 42 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8512 (mt-10) REVERT: F 209 PHE cc_start: 0.9633 (m-10) cc_final: 0.9284 (m-80) REVERT: F 214 LEU cc_start: 0.9736 (OUTLIER) cc_final: 0.9512 (mt) REVERT: F 227 GLU cc_start: 0.9822 (mm-30) cc_final: 0.9520 (mm-30) outliers start: 5 outliers final: 1 residues processed: 288 average time/residue: 0.1111 time to fit residues: 42.9600 Evaluate side-chains 279 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 275 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 20 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN ** F 63 ASN ** 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 = 0.3187 r_free = 0.3187 target = 0.053786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.043688 restraints weight = 62925.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.044699 restraints weight = 45046.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.045389 restraints weight = 35008.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.045928 restraints weight = 28953.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.046311 restraints weight = 24999.091| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.6894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9522 Z= 0.202 Angle : 1.094 17.176 12936 Z= 0.564 Chirality : 0.049 0.211 1476 Planarity : 0.005 0.039 1548 Dihedral : 4.350 20.416 1218 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 27.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.69 % Allowed : 35.29 % Favored : 64.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.24), residues: 1110 helix: 0.97 (0.18), residues: 822 sheet: 1.36 (0.61), residues: 60 loop : -1.89 (0.34), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 33 TYR 0.022 0.002 TYR F 230 PHE 0.027 0.002 PHE F 212 TRP 0.085 0.002 TRP C 78 HIS 0.003 0.001 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 9504) covalent geometry : angle 1.09537 (12900) SS BOND : bond 0.00189 ( 18) SS BOND : angle 0.67668 ( 36) hydrogen bonds : bond 0.05120 ( 684) hydrogen bonds : angle 5.47525 ( 2034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1733.59 seconds wall clock time: 30 minutes 49.64 seconds (1849.64 seconds total)