Starting phenix.real_space_refine on Wed Mar 4 19:32:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d9m_27266/03_2026/8d9m_27266.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d9m_27266/03_2026/8d9m_27266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d9m_27266/03_2026/8d9m_27266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d9m_27266/03_2026/8d9m_27266.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d9m_27266/03_2026/8d9m_27266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d9m_27266/03_2026/8d9m_27266.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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: 5 Type Number sf(0) Gaussians Fe 56 7.16 5 S 126 5.16 5 C 10276 2.51 5 N 2660 2.21 5 O 2849 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15967 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1937 Classifications: {'peptide': 258} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 236} Chain: "B" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 344 Unusual residues: {'HEC': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Restraints were copied for chains: C, D, A, E, F, G Time building chain proxies: 2.13, per 1000 atoms: 0.13 Number of scatterers: 15967 At special positions: 0 Unit cell: (81, 81, 438.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 56 26.01 S 126 16.00 O 2849 8.00 N 2660 7.00 C 10276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=180, symmetry=0 Number of additional bonds: simple=180, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 798.7 milliseconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3318 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 14 sheets defined 19.4% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 57 through 67 removed outlier: 3.724A pdb=" N VAL A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 67 " --> pdb=" O GLN A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 201 through 206 Processing helix chain 'A' and resid 224 through 230 removed outlier: 3.522A pdb=" N GLN A 228 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 268 through 277 removed outlier: 3.528A pdb=" N CYS A 272 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 67 removed outlier: 3.725A pdb=" N VAL B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 67 " --> pdb=" O GLN B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 71 Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 201 through 206 Processing helix chain 'B' and resid 224 through 230 removed outlier: 3.522A pdb=" N GLN B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 268 through 277 removed outlier: 3.528A pdb=" N CYS B 272 " --> pdb=" O ASN B 268 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 67 removed outlier: 3.724A pdb=" N VAL C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 67 " --> pdb=" O GLN C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 71 Processing helix chain 'C' and resid 123 through 128 Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 224 through 230 removed outlier: 3.522A pdb=" N GLN C 228 " --> pdb=" O VAL C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 268 through 277 removed outlier: 3.527A pdb=" N CYS C 272 " --> pdb=" O ASN C 268 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 67 removed outlier: 3.724A pdb=" N VAL D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 67 " --> pdb=" O GLN D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 71 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 201 through 206 Processing helix chain 'D' and resid 224 through 230 removed outlier: 3.522A pdb=" N GLN D 228 " --> pdb=" O VAL D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'D' and resid 268 through 277 removed outlier: 3.529A pdb=" N CYS D 272 " --> pdb=" O ASN D 268 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 67 removed outlier: 3.725A pdb=" N VAL E 61 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU E 67 " --> pdb=" O GLN E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 71 Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 201 through 206 Processing helix chain 'E' and resid 224 through 230 removed outlier: 3.522A pdb=" N GLN E 228 " --> pdb=" O VAL E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 239 Processing helix chain 'E' and resid 268 through 277 removed outlier: 3.528A pdb=" N CYS E 272 " --> pdb=" O ASN E 268 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS E 275 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 67 removed outlier: 3.724A pdb=" N VAL F 61 " --> pdb=" O ASP F 57 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU F 67 " --> pdb=" O GLN F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 71 Processing helix chain 'F' and resid 123 through 128 Processing helix chain 'F' and resid 201 through 206 Processing helix chain 'F' and resid 224 through 230 removed outlier: 3.522A pdb=" N GLN F 228 " --> pdb=" O VAL F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 239 Processing helix chain 'F' and resid 268 through 277 removed outlier: 3.528A pdb=" N CYS F 272 " --> pdb=" O ASN F 268 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS F 275 " --> pdb=" O ASP F 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 67 removed outlier: 3.724A pdb=" N VAL G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU G 67 " --> pdb=" O GLN G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 71 Processing helix chain 'G' and resid 123 through 128 Processing helix chain 'G' and resid 201 through 206 Processing helix chain 'G' and resid 224 through 230 removed outlier: 3.521A pdb=" N GLN G 228 " --> pdb=" O VAL G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 239 Processing helix chain 'G' and resid 268 through 277 removed outlier: 3.529A pdb=" N CYS G 272 " --> pdb=" O ASN G 268 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS G 275 " --> pdb=" O ASP G 271 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 95 through 97 Processing sheet with id=2, first strand: chain 'A' and resid 185 through 189 removed outlier: 4.996A pdb=" N ILE A 199 " --> pdb=" O PRO A 186 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 95 through 97 Processing sheet with id=4, first strand: chain 'B' and resid 185 through 189 removed outlier: 4.996A pdb=" N ILE B 199 " --> pdb=" O PRO B 186 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'C' and resid 95 through 97 Processing sheet with id=6, first strand: chain 'C' and resid 185 through 189 removed outlier: 4.996A pdb=" N ILE C 199 " --> pdb=" O PRO C 186 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'D' and resid 95 through 97 Processing sheet with id=8, first strand: chain 'D' and resid 185 through 189 removed outlier: 4.996A pdb=" N ILE D 199 " --> pdb=" O PRO D 186 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'E' and resid 95 through 97 Processing sheet with id=10, first strand: chain 'E' and resid 185 through 189 removed outlier: 4.996A pdb=" N ILE E 199 " --> pdb=" O PRO E 186 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'F' and resid 95 through 97 Processing sheet with id=12, first strand: chain 'F' and resid 185 through 189 removed outlier: 4.996A pdb=" N ILE F 199 " --> pdb=" O PRO F 186 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'G' and resid 95 through 97 Processing sheet with id=14, first strand: chain 'G' and resid 185 through 189 removed outlier: 4.996A pdb=" N ILE G 199 " --> pdb=" O PRO G 186 " (cutoff:3.500A) 154 hydrogen bonds defined for protein. 441 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 6902 1.39 - 1.56: 9499 1.56 - 1.73: 7 1.73 - 1.90: 140 1.90 - 2.08: 224 Bond restraints: 16772 Sorted by residual: bond pdb=" CA ALA G 89 " pdb=" C ALA G 89 " ideal model delta sigma weight residual 1.524 1.484 0.040 1.48e-02 4.57e+03 7.33e+00 bond pdb=" CA ALA C 89 " pdb=" C ALA C 89 " ideal model delta sigma weight residual 1.524 1.485 0.040 1.48e-02 4.57e+03 7.27e+00 bond pdb=" CA ALA E 89 " pdb=" C ALA E 89 " ideal model delta sigma weight residual 1.524 1.485 0.040 1.48e-02 4.57e+03 7.22e+00 bond pdb=" CA ALA B 89 " pdb=" C ALA B 89 " ideal model delta sigma weight residual 1.524 1.485 0.040 1.48e-02 4.57e+03 7.17e+00 bond pdb=" CA ALA A 89 " pdb=" C ALA A 89 " ideal model delta sigma weight residual 1.524 1.485 0.040 1.48e-02 4.57e+03 7.14e+00 ... (remaining 16767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 21868 1.65 - 3.29: 1460 3.29 - 4.94: 262 4.94 - 6.59: 140 6.59 - 8.23: 35 Bond angle restraints: 23765 Sorted by residual: angle pdb=" N ALA D 89 " pdb=" CA ALA D 89 " pdb=" C ALA D 89 " ideal model delta sigma weight residual 112.72 107.01 5.71 1.14e+00 7.69e-01 2.51e+01 angle pdb=" N ALA A 89 " pdb=" CA ALA A 89 " pdb=" C ALA A 89 " ideal model delta sigma weight residual 112.72 107.02 5.70 1.14e+00 7.69e-01 2.50e+01 angle pdb=" N ALA B 89 " pdb=" CA ALA B 89 " pdb=" C ALA B 89 " ideal model delta sigma weight residual 112.72 107.03 5.69 1.14e+00 7.69e-01 2.49e+01 angle pdb=" N ALA E 89 " pdb=" CA ALA E 89 " pdb=" C ALA E 89 " ideal model delta sigma weight residual 112.72 107.03 5.69 1.14e+00 7.69e-01 2.49e+01 angle pdb=" N ALA G 89 " pdb=" CA ALA G 89 " pdb=" C ALA G 89 " ideal model delta sigma weight residual 112.72 107.04 5.68 1.14e+00 7.69e-01 2.49e+01 ... (remaining 23760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 7805 17.06 - 34.12: 532 34.12 - 51.18: 140 51.18 - 68.24: 70 68.24 - 85.30: 70 Dihedral angle restraints: 8617 sinusoidal: 3472 harmonic: 5145 Sorted by residual: dihedral pdb=" CA PRO E 29 " pdb=" C PRO E 29 " pdb=" N PRO E 30 " pdb=" CA PRO E 30 " ideal model delta harmonic sigma weight residual 180.00 149.12 30.88 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA PRO D 29 " pdb=" C PRO D 29 " pdb=" N PRO D 30 " pdb=" CA PRO D 30 " ideal model delta harmonic sigma weight residual 180.00 149.14 30.86 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA PRO F 29 " pdb=" C PRO F 29 " pdb=" N PRO F 30 " pdb=" CA PRO F 30 " ideal model delta harmonic sigma weight residual 180.00 149.14 30.86 0 5.00e+00 4.00e-02 3.81e+01 ... (remaining 8614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1530 0.053 - 0.106: 503 0.106 - 0.159: 83 0.159 - 0.211: 5 0.211 - 0.264: 7 Chirality restraints: 2128 Sorted by residual: chirality pdb=" CA LEU F 88 " pdb=" N LEU F 88 " pdb=" C LEU F 88 " pdb=" CB LEU F 88 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA LEU B 88 " pdb=" N LEU B 88 " pdb=" C LEU B 88 " pdb=" CB LEU B 88 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA LEU E 88 " pdb=" N LEU E 88 " pdb=" C LEU E 88 " pdb=" CB LEU E 88 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 2125 not shown) Planarity restraints: 2912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 87 " -0.026 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C THR C 87 " 0.094 2.00e-02 2.50e+03 pdb=" O THR C 87 " -0.037 2.00e-02 2.50e+03 pdb=" N LEU C 88 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 87 " 0.026 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C THR D 87 " -0.094 2.00e-02 2.50e+03 pdb=" O THR D 87 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU D 88 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 87 " 0.026 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C THR F 87 " -0.094 2.00e-02 2.50e+03 pdb=" O THR F 87 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU F 88 " 0.031 2.00e-02 2.50e+03 ... (remaining 2909 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 119 2.33 - 2.97: 8157 2.97 - 3.61: 25220 3.61 - 4.26: 36775 4.26 - 4.90: 57179 Nonbonded interactions: 127450 Sorted by model distance: nonbonded pdb=" CE1 HIS F 207 " pdb="FE HEC F 606 " model vdw 1.684 3.220 nonbonded pdb=" CE1 HIS G 207 " pdb="FE HEC G 606 " model vdw 1.684 3.220 nonbonded pdb=" CE1 HIS B 207 " pdb="FE HEC B 606 " model vdw 1.684 3.220 nonbonded pdb=" CE1 HIS A 207 " pdb="FE HEC A 606 " model vdw 1.684 3.220 nonbonded pdb=" CE1 HIS E 207 " pdb="FE HEC E 606 " model vdw 1.684 3.220 ... (remaining 127445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'A' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.610 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.024 0.469 16952 Z= 2.107 Angle : 1.023 8.233 23765 Z= 0.459 Chirality : 0.051 0.264 2128 Planarity : 0.008 0.116 2912 Dihedral : 16.461 85.304 5299 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 29.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.19 % Favored : 82.81 % Rotamer: Outliers : 0.45 % Allowed : 0.45 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.19), residues: 1792 helix: -1.74 (0.25), residues: 294 sheet: -1.24 (0.28), residues: 154 loop : -1.93 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 227 TYR 0.012 0.003 TYR E 147 PHE 0.021 0.003 PHE G 42 TRP 0.016 0.002 TRP G 270 HIS 0.015 0.002 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00738 (16772) covalent geometry : angle 1.02295 (23765) hydrogen bonds : bond 0.17048 ( 154) hydrogen bonds : angle 8.92912 ( 441) Misc. bond : bond 0.21764 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 408 time to evaluate : 0.442 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 VAL cc_start: 0.9141 (m) cc_final: 0.8909 (p) REVERT: B 79 ASN cc_start: 0.7926 (t0) cc_final: 0.7482 (t0) REVERT: B 95 MET cc_start: 0.8634 (mmm) cc_final: 0.8231 (mmm) REVERT: B 129 LYS cc_start: 0.9358 (ptpp) cc_final: 0.8984 (mttp) REVERT: B 176 GLN cc_start: 0.7279 (tm-30) cc_final: 0.7053 (tm-30) REVERT: B 203 GLN cc_start: 0.8910 (tp40) cc_final: 0.8348 (tp40) REVERT: B 204 ASP cc_start: 0.8815 (m-30) cc_final: 0.8484 (m-30) REVERT: B 269 ASN cc_start: 0.8206 (m-40) cc_final: 0.7723 (t0) REVERT: B 277 TRP cc_start: 0.8260 (t-100) cc_final: 0.7741 (t-100) REVERT: C 51 LEU cc_start: 0.7716 (mt) cc_final: 0.7514 (mt) REVERT: C 79 ASN cc_start: 0.7750 (t0) cc_final: 0.7431 (t0) REVERT: C 95 MET cc_start: 0.8712 (mmm) cc_final: 0.8128 (mmp) REVERT: C 116 THR cc_start: 0.8837 (m) cc_final: 0.8338 (t) REVERT: C 148 ILE cc_start: 0.9148 (mm) cc_final: 0.8879 (mm) REVERT: C 179 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7394 (mt-10) REVERT: C 203 GLN cc_start: 0.8920 (tp40) cc_final: 0.8226 (tp40) REVERT: C 216 LEU cc_start: 0.8639 (tp) cc_final: 0.8395 (mp) REVERT: C 269 ASN cc_start: 0.8340 (m-40) cc_final: 0.7806 (m-40) REVERT: D 51 LEU cc_start: 0.7633 (mt) cc_final: 0.7421 (mt) REVERT: D 79 ASN cc_start: 0.7874 (t0) cc_final: 0.7502 (t0) REVERT: D 108 PHE cc_start: 0.8734 (p90) cc_final: 0.8469 (p90) REVERT: D 133 TYR cc_start: 0.8739 (t80) cc_final: 0.8533 (t80) REVERT: D 179 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7590 (mt-10) REVERT: D 203 GLN cc_start: 0.8905 (tp40) cc_final: 0.8301 (tp40) REVERT: D 216 LEU cc_start: 0.8666 (tp) cc_final: 0.8459 (mp) REVERT: D 269 ASN cc_start: 0.8414 (m-40) cc_final: 0.7939 (m-40) REVERT: A 37 ILE cc_start: 0.8675 (pt) cc_final: 0.8428 (pt) REVERT: A 61 VAL cc_start: 0.9207 (m) cc_final: 0.9007 (p) REVERT: A 176 GLN cc_start: 0.7590 (tm-30) cc_final: 0.7111 (tm-30) REVERT: A 203 GLN cc_start: 0.9054 (tp40) cc_final: 0.8529 (tp40) REVERT: A 226 ILE cc_start: 0.8978 (tp) cc_final: 0.8733 (tp) REVERT: A 230 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7504 (mt-10) REVERT: A 269 ASN cc_start: 0.8214 (m-40) cc_final: 0.7703 (m-40) REVERT: E 61 VAL cc_start: 0.9144 (m) cc_final: 0.8927 (p) REVERT: E 79 ASN cc_start: 0.7914 (t0) cc_final: 0.7388 (t0) REVERT: E 95 MET cc_start: 0.8653 (mmm) cc_final: 0.8449 (mmm) REVERT: E 148 ILE cc_start: 0.9194 (mm) cc_final: 0.8987 (mm) REVERT: E 179 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7363 (mt-10) REVERT: E 203 GLN cc_start: 0.8933 (tp40) cc_final: 0.8543 (tp40) REVERT: E 204 ASP cc_start: 0.8724 (m-30) cc_final: 0.8522 (m-30) REVERT: E 269 ASN cc_start: 0.8388 (m-40) cc_final: 0.7526 (t0) REVERT: E 273 GLN cc_start: 0.8770 (mt0) cc_final: 0.8495 (mt0) REVERT: F 79 ASN cc_start: 0.7905 (t0) cc_final: 0.7598 (t0) REVERT: F 95 MET cc_start: 0.8712 (mmm) cc_final: 0.8372 (mmm) REVERT: F 108 PHE cc_start: 0.8878 (p90) cc_final: 0.8555 (p90) REVERT: F 176 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7377 (tm-30) REVERT: F 204 ASP cc_start: 0.8773 (m-30) cc_final: 0.8570 (m-30) REVERT: F 269 ASN cc_start: 0.8581 (m-40) cc_final: 0.8047 (m-40) REVERT: G 37 ILE cc_start: 0.8742 (pt) cc_final: 0.8505 (pt) REVERT: G 79 ASN cc_start: 0.7957 (t0) cc_final: 0.7669 (t0) REVERT: G 107 ASP cc_start: 0.8263 (t70) cc_final: 0.8020 (t0) REVERT: G 141 ASN cc_start: 0.8852 (t0) cc_final: 0.8600 (t0) REVERT: G 203 GLN cc_start: 0.9043 (tp40) cc_final: 0.8393 (tp40) REVERT: G 204 ASP cc_start: 0.8831 (m-30) cc_final: 0.8593 (m-30) REVERT: G 216 LEU cc_start: 0.8629 (tp) cc_final: 0.8381 (mt) REVERT: G 269 ASN cc_start: 0.8420 (m-40) cc_final: 0.7827 (m-40) outliers start: 7 outliers final: 7 residues processed: 415 average time/residue: 0.1393 time to fit residues: 83.3858 Evaluate side-chains 361 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 354 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN D 146 HIS D 273 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS E 228 GLN F 273 GLN G 63 GLN G 146 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.084483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.069149 restraints weight = 45879.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.072076 restraints weight = 26750.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.074145 restraints weight = 17995.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.075617 restraints weight = 13235.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.076688 restraints weight = 10377.186| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.467 16952 Z= 0.252 Angle : 1.011 15.811 23765 Z= 0.364 Chirality : 0.048 0.145 2128 Planarity : 0.006 0.070 2912 Dihedral : 17.970 89.853 2303 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.19), residues: 1792 helix: -1.47 (0.28), residues: 287 sheet: -1.32 (0.33), residues: 154 loop : -1.85 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 163 TYR 0.013 0.002 TYR E 133 PHE 0.016 0.002 PHE C 105 TRP 0.018 0.002 TRP F 279 HIS 0.008 0.001 HIS G 276 Details of bonding type rmsd covalent geometry : bond 0.00703 (16772) covalent geometry : angle 1.01057 (23765) hydrogen bonds : bond 0.03138 ( 154) hydrogen bonds : angle 6.58563 ( 441) Misc. bond : bond 0.17109 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 0.642 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 LEU cc_start: 0.7709 (mt) cc_final: 0.7498 (mt) REVERT: B 60 LEU cc_start: 0.9159 (mm) cc_final: 0.8882 (pp) REVERT: B 61 VAL cc_start: 0.9283 (m) cc_final: 0.9068 (p) REVERT: B 63 GLN cc_start: 0.8740 (mt0) cc_final: 0.8406 (mt0) REVERT: B 95 MET cc_start: 0.8443 (mmm) cc_final: 0.8097 (mmm) REVERT: B 129 LYS cc_start: 0.9362 (ptpp) cc_final: 0.9068 (mttp) REVERT: B 203 GLN cc_start: 0.9031 (tp40) cc_final: 0.8342 (tp40) REVERT: B 204 ASP cc_start: 0.8952 (m-30) cc_final: 0.8541 (m-30) REVERT: B 238 LEU cc_start: 0.8989 (mp) cc_final: 0.8756 (mp) REVERT: B 243 LYS cc_start: 0.8831 (tmtt) cc_final: 0.8615 (tptp) REVERT: B 263 TRP cc_start: 0.8347 (m100) cc_final: 0.7873 (m100) REVERT: B 269 ASN cc_start: 0.8135 (m-40) cc_final: 0.7416 (t0) REVERT: B 273 GLN cc_start: 0.8589 (mt0) cc_final: 0.8301 (mt0) REVERT: C 51 LEU cc_start: 0.7555 (mt) cc_final: 0.7332 (mt) REVERT: C 79 ASN cc_start: 0.7889 (t0) cc_final: 0.7414 (t0) REVERT: C 95 MET cc_start: 0.8583 (mmm) cc_final: 0.8189 (mmm) REVERT: C 108 PHE cc_start: 0.8924 (p90) cc_final: 0.8412 (p90) REVERT: C 116 THR cc_start: 0.8884 (m) cc_final: 0.8224 (t) REVERT: C 117 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8106 (mm-40) REVERT: C 139 ILE cc_start: 0.8738 (tp) cc_final: 0.8527 (tp) REVERT: C 179 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7592 (mt-10) REVERT: C 182 HIS cc_start: 0.8279 (m-70) cc_final: 0.7813 (m-70) REVERT: C 183 GLN cc_start: 0.4856 (pm20) cc_final: 0.4554 (pm20) REVERT: C 203 GLN cc_start: 0.9022 (tp40) cc_final: 0.8280 (tp40) REVERT: C 238 LEU cc_start: 0.8846 (mp) cc_final: 0.8543 (mt) REVERT: C 269 ASN cc_start: 0.7560 (m-40) cc_final: 0.6933 (t0) REVERT: C 279 TRP cc_start: 0.7753 (t-100) cc_final: 0.7495 (t-100) REVERT: D 79 ASN cc_start: 0.7987 (t0) cc_final: 0.7668 (t0) REVERT: D 108 PHE cc_start: 0.8857 (p90) cc_final: 0.8618 (p90) REVERT: D 176 GLN cc_start: 0.7375 (tm-30) cc_final: 0.7010 (tm-30) REVERT: D 203 GLN cc_start: 0.9063 (tp40) cc_final: 0.8466 (tp40) REVERT: D 204 ASP cc_start: 0.8886 (m-30) cc_final: 0.8554 (m-30) REVERT: D 230 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7718 (mt-10) REVERT: D 242 GLN cc_start: 0.8115 (tp40) cc_final: 0.7823 (tp-100) REVERT: D 269 ASN cc_start: 0.7800 (m-40) cc_final: 0.7232 (t0) REVERT: A 34 PHE cc_start: 0.8697 (p90) cc_final: 0.8481 (p90) REVERT: A 37 ILE cc_start: 0.8619 (pt) cc_final: 0.8418 (pt) REVERT: A 51 LEU cc_start: 0.7609 (mt) cc_final: 0.7386 (mt) REVERT: A 61 VAL cc_start: 0.9314 (m) cc_final: 0.9079 (p) REVERT: A 176 GLN cc_start: 0.7565 (tm-30) cc_final: 0.7164 (tm-30) REVERT: A 203 GLN cc_start: 0.9007 (tp40) cc_final: 0.8599 (tp40) REVERT: A 204 ASP cc_start: 0.8813 (m-30) cc_final: 0.8572 (m-30) REVERT: A 226 ILE cc_start: 0.8980 (tp) cc_final: 0.8698 (tp) REVERT: A 227 ARG cc_start: 0.9004 (mtt180) cc_final: 0.8508 (mtt180) REVERT: A 230 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7512 (mt-10) REVERT: A 269 ASN cc_start: 0.7690 (m-40) cc_final: 0.7329 (t0) REVERT: E 51 LEU cc_start: 0.7825 (mt) cc_final: 0.7579 (mt) REVERT: E 63 GLN cc_start: 0.8754 (mt0) cc_final: 0.8508 (mt0) REVERT: E 79 ASN cc_start: 0.8103 (t0) cc_final: 0.7811 (t0) REVERT: E 129 LYS cc_start: 0.9169 (ptpp) cc_final: 0.8906 (mttp) REVERT: E 133 TYR cc_start: 0.8802 (t80) cc_final: 0.8562 (t80) REVERT: E 176 GLN cc_start: 0.7553 (tm-30) cc_final: 0.7114 (tm-30) REVERT: E 203 GLN cc_start: 0.8993 (tp40) cc_final: 0.8606 (tp40) REVERT: E 204 ASP cc_start: 0.8634 (m-30) cc_final: 0.8372 (m-30) REVERT: E 242 GLN cc_start: 0.8000 (tp40) cc_final: 0.7566 (tp-100) REVERT: E 266 ILE cc_start: 0.8581 (mp) cc_final: 0.8271 (mp) REVERT: E 273 GLN cc_start: 0.8690 (mt0) cc_final: 0.8434 (mt0) REVERT: F 51 LEU cc_start: 0.7591 (mt) cc_final: 0.7369 (mt) REVERT: F 79 ASN cc_start: 0.7892 (t0) cc_final: 0.7591 (t0) REVERT: F 95 MET cc_start: 0.8619 (mmm) cc_final: 0.8314 (mmm) REVERT: F 108 PHE cc_start: 0.8988 (p90) cc_final: 0.8660 (p90) REVERT: F 176 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7376 (tm-30) REVERT: F 203 GLN cc_start: 0.8974 (tp40) cc_final: 0.8609 (tp40) REVERT: F 204 ASP cc_start: 0.8917 (m-30) cc_final: 0.8508 (m-30) REVERT: F 226 ILE cc_start: 0.9035 (tp) cc_final: 0.8803 (tp) REVERT: F 228 GLN cc_start: 0.8780 (tt0) cc_final: 0.8405 (tm-30) REVERT: F 230 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7595 (mt-10) REVERT: F 243 LYS cc_start: 0.8797 (tmtt) cc_final: 0.8585 (tptp) REVERT: F 263 TRP cc_start: 0.8521 (m100) cc_final: 0.7874 (m100) REVERT: F 269 ASN cc_start: 0.7794 (m-40) cc_final: 0.7375 (t0) REVERT: G 37 ILE cc_start: 0.8571 (pt) cc_final: 0.8197 (pt) REVERT: G 46 THR cc_start: 0.8147 (t) cc_final: 0.7678 (p) REVERT: G 79 ASN cc_start: 0.7914 (t0) cc_final: 0.7643 (t0) REVERT: G 108 PHE cc_start: 0.9125 (p90) cc_final: 0.8757 (p90) REVERT: G 140 ASP cc_start: 0.8370 (m-30) cc_final: 0.8066 (t0) REVERT: G 141 ASN cc_start: 0.8762 (t0) cc_final: 0.8445 (t0) REVERT: G 179 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7569 (mt-10) REVERT: G 182 HIS cc_start: 0.8561 (m-70) cc_final: 0.7852 (m170) REVERT: G 204 ASP cc_start: 0.9000 (m-30) cc_final: 0.8590 (m-30) REVERT: G 216 LEU cc_start: 0.8774 (tp) cc_final: 0.8484 (mt) REVERT: G 226 ILE cc_start: 0.8921 (tp) cc_final: 0.8677 (tp) REVERT: G 230 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7815 (mt-10) REVERT: G 238 LEU cc_start: 0.8894 (mt) cc_final: 0.8612 (mt) REVERT: G 241 ILE cc_start: 0.8862 (pt) cc_final: 0.8552 (pt) REVERT: G 242 GLN cc_start: 0.7871 (tp40) cc_final: 0.7467 (tp-100) REVERT: G 244 ASP cc_start: 0.8118 (t0) cc_final: 0.7423 (t0) REVERT: G 269 ASN cc_start: 0.7612 (m-40) cc_final: 0.6983 (t0) REVERT: G 279 TRP cc_start: 0.7779 (t-100) cc_final: 0.7466 (t-100) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.1275 time to fit residues: 81.4432 Evaluate side-chains 402 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 82 optimal weight: 0.9980 chunk 136 optimal weight: 0.3980 chunk 135 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 143 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 64 optimal weight: 0.0570 chunk 147 optimal weight: 0.0870 chunk 120 optimal weight: 0.8980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN B 135 HIS ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 228 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN A 135 HIS A 228 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 GLN E 146 HIS ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN F 135 HIS ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 273 GLN G 63 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.088981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.073206 restraints weight = 44765.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.076452 restraints weight = 25089.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.078715 restraints weight = 16274.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.080311 restraints weight = 11631.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.081493 restraints weight = 8927.390| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.314 16952 Z= 0.149 Angle : 0.838 10.213 23765 Z= 0.328 Chirality : 0.047 0.154 2128 Planarity : 0.005 0.058 2912 Dihedral : 17.797 89.861 2303 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.72 % Favored : 87.28 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.20), residues: 1792 helix: -1.60 (0.27), residues: 287 sheet: None (None), residues: 0 loop : -1.36 (0.17), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 109 TYR 0.016 0.002 TYR A 133 PHE 0.013 0.001 PHE F 103 TRP 0.017 0.001 TRP F 279 HIS 0.006 0.001 HIS G 276 Details of bonding type rmsd covalent geometry : bond 0.00422 (16772) covalent geometry : angle 0.83755 (23765) hydrogen bonds : bond 0.02886 ( 154) hydrogen bonds : angle 6.34568 ( 441) Misc. bond : bond 0.09583 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 0.352 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: 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: B 51 LEU cc_start: 0.7382 (mt) cc_final: 0.7164 (mt) REVERT: B 63 GLN cc_start: 0.8776 (mt0) cc_final: 0.8375 (mt0) REVERT: B 79 ASN cc_start: 0.7837 (t0) cc_final: 0.7330 (t0) REVERT: B 95 MET cc_start: 0.8431 (mmm) cc_final: 0.8180 (mmm) REVERT: B 117 GLN cc_start: 0.8743 (tp-100) cc_final: 0.8454 (tp40) REVERT: B 129 LYS cc_start: 0.9292 (ptpp) cc_final: 0.9052 (mttp) REVERT: B 135 HIS cc_start: 0.7247 (p90) cc_final: 0.6758 (p-80) REVERT: B 183 GLN cc_start: 0.7365 (pm20) cc_final: 0.7107 (pm20) REVERT: B 204 ASP cc_start: 0.8808 (m-30) cc_final: 0.7843 (t0) REVERT: B 238 LEU cc_start: 0.9093 (mp) cc_final: 0.8869 (mp) REVERT: C 79 ASN cc_start: 0.7707 (t0) cc_final: 0.7382 (t0) REVERT: C 90 THR cc_start: 0.8409 (p) cc_final: 0.8174 (t) REVERT: C 95 MET cc_start: 0.8378 (mmm) cc_final: 0.7938 (mmp) REVERT: C 108 PHE cc_start: 0.8941 (p90) cc_final: 0.8444 (p90) REVERT: C 116 THR cc_start: 0.8864 (m) cc_final: 0.8244 (t) REVERT: C 117 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8015 (mm110) REVERT: C 179 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7261 (mt-10) REVERT: C 182 HIS cc_start: 0.8122 (m-70) cc_final: 0.7332 (m-70) REVERT: C 183 GLN cc_start: 0.6613 (pm20) cc_final: 0.5928 (pm20) REVERT: C 203 GLN cc_start: 0.8965 (tp40) cc_final: 0.8181 (tp40) REVERT: C 204 ASP cc_start: 0.8694 (m-30) cc_final: 0.8420 (m-30) REVERT: C 263 TRP cc_start: 0.8310 (m100) cc_final: 0.7558 (m100) REVERT: C 269 ASN cc_start: 0.7382 (m-40) cc_final: 0.6775 (m-40) REVERT: C 279 TRP cc_start: 0.7746 (t-100) cc_final: 0.7498 (t-100) REVERT: D 51 LEU cc_start: 0.7320 (mt) cc_final: 0.7101 (mt) REVERT: D 79 ASN cc_start: 0.7870 (t0) cc_final: 0.7502 (t0) REVERT: D 108 PHE cc_start: 0.8815 (p90) cc_final: 0.8396 (p90) REVERT: D 203 GLN cc_start: 0.9026 (tp40) cc_final: 0.8417 (tp40) REVERT: D 204 ASP cc_start: 0.8782 (m-30) cc_final: 0.8444 (m-30) REVERT: D 226 ILE cc_start: 0.9001 (tp) cc_final: 0.8717 (tp) REVERT: D 227 ARG cc_start: 0.8909 (mtt180) cc_final: 0.8639 (mtt180) REVERT: D 230 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7629 (mt-10) REVERT: D 269 ASN cc_start: 0.7679 (m-40) cc_final: 0.7330 (m-40) REVERT: A 37 ILE cc_start: 0.8455 (pt) cc_final: 0.8176 (pt) REVERT: A 108 PHE cc_start: 0.8836 (p90) cc_final: 0.8494 (p90) REVERT: A 129 LYS cc_start: 0.9305 (ptpp) cc_final: 0.8956 (mtmm) REVERT: A 141 ASN cc_start: 0.8643 (t0) cc_final: 0.8236 (t0) REVERT: A 144 ASP cc_start: 0.7890 (p0) cc_final: 0.7438 (p0) REVERT: A 146 HIS cc_start: 0.8119 (p-80) cc_final: 0.7866 (p90) REVERT: A 176 GLN cc_start: 0.7607 (tm-30) cc_final: 0.7322 (tm-30) REVERT: A 203 GLN cc_start: 0.8895 (tp40) cc_final: 0.8551 (tp40) REVERT: A 204 ASP cc_start: 0.8800 (m-30) cc_final: 0.8522 (m-30) REVERT: A 226 ILE cc_start: 0.8977 (tp) cc_final: 0.8667 (tp) REVERT: A 227 ARG cc_start: 0.8787 (mtt180) cc_final: 0.8329 (mtt180) REVERT: A 230 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7268 (mt-10) REVERT: A 269 ASN cc_start: 0.7495 (m-40) cc_final: 0.6970 (m-40) REVERT: E 37 ILE cc_start: 0.8367 (pt) cc_final: 0.8121 (pt) REVERT: E 62 GLN cc_start: 0.8637 (mm110) cc_final: 0.8308 (mp10) REVERT: E 63 GLN cc_start: 0.8831 (mt0) cc_final: 0.8498 (mt0) REVERT: E 79 ASN cc_start: 0.7973 (t0) cc_final: 0.7425 (t0) REVERT: E 108 PHE cc_start: 0.8828 (p90) cc_final: 0.8555 (p90) REVERT: E 133 TYR cc_start: 0.8779 (t80) cc_final: 0.8432 (t80) REVERT: E 135 HIS cc_start: 0.7692 (p-80) cc_final: 0.7309 (p-80) REVERT: E 204 ASP cc_start: 0.8580 (m-30) cc_final: 0.8281 (m-30) REVERT: E 213 ASP cc_start: 0.8402 (t0) cc_final: 0.8191 (t0) REVERT: E 269 ASN cc_start: 0.7992 (m-40) cc_final: 0.7005 (m-40) REVERT: F 79 ASN cc_start: 0.7645 (t0) cc_final: 0.7320 (t0) REVERT: F 106 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8635 (tm-30) REVERT: F 108 PHE cc_start: 0.8883 (p90) cc_final: 0.8459 (p90) REVERT: F 116 THR cc_start: 0.8983 (t) cc_final: 0.8731 (t) REVERT: F 129 LYS cc_start: 0.9190 (mttp) cc_final: 0.8872 (mttp) REVERT: F 203 GLN cc_start: 0.8926 (tp40) cc_final: 0.8563 (tp40) REVERT: F 204 ASP cc_start: 0.8850 (m-30) cc_final: 0.8402 (m-30) REVERT: F 216 LEU cc_start: 0.8970 (tt) cc_final: 0.8364 (mt) REVERT: F 226 ILE cc_start: 0.8987 (tp) cc_final: 0.8667 (tp) REVERT: F 230 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7587 (mt-10) REVERT: F 243 LYS cc_start: 0.8784 (tmtt) cc_final: 0.8459 (tptp) REVERT: F 255 LYS cc_start: 0.8619 (ptpp) cc_final: 0.8398 (ptpp) REVERT: F 263 TRP cc_start: 0.8466 (m100) cc_final: 0.7887 (m100) REVERT: F 269 ASN cc_start: 0.7543 (m-40) cc_final: 0.6897 (m-40) REVERT: F 279 TRP cc_start: 0.7700 (t-100) cc_final: 0.7389 (t-100) REVERT: G 79 ASN cc_start: 0.7863 (t0) cc_final: 0.7411 (t0) REVERT: G 108 PHE cc_start: 0.9194 (p90) cc_final: 0.8596 (p90) REVERT: G 116 THR cc_start: 0.8817 (t) cc_final: 0.8384 (t) REVERT: G 117 GLN cc_start: 0.8343 (mm110) cc_final: 0.8113 (mm110) REVERT: G 129 LYS cc_start: 0.9255 (ptpp) cc_final: 0.8990 (mttt) REVERT: G 179 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7046 (mt-10) REVERT: G 203 GLN cc_start: 0.9050 (tp40) cc_final: 0.8175 (tp40) REVERT: G 204 ASP cc_start: 0.8864 (m-30) cc_final: 0.8483 (m-30) REVERT: G 231 VAL cc_start: 0.8627 (t) cc_final: 0.8383 (p) REVERT: G 238 LEU cc_start: 0.8982 (mt) cc_final: 0.8712 (mp) REVERT: G 241 ILE cc_start: 0.8840 (pt) cc_final: 0.8537 (pt) REVERT: G 242 GLN cc_start: 0.7989 (tp40) cc_final: 0.7658 (tp-100) REVERT: G 260 ASP cc_start: 0.7972 (t0) cc_final: 0.7685 (t0) REVERT: G 263 TRP cc_start: 0.8210 (m100) cc_final: 0.7826 (m100) REVERT: G 269 ASN cc_start: 0.7475 (m-40) cc_final: 0.6884 (m-40) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.1303 time to fit residues: 82.1504 Evaluate side-chains 388 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 0.0470 chunk 136 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 149 optimal weight: 0.2980 chunk 90 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN C 228 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS D 228 GLN D 273 GLN A 117 GLN ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 GLN F 63 GLN F 228 GLN ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 135 HIS G 228 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.086741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.071505 restraints weight = 45289.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.074513 restraints weight = 26054.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.076605 restraints weight = 17269.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.078123 restraints weight = 12556.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.079244 restraints weight = 9753.154| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.470 16952 Z= 0.185 Angle : 0.847 10.238 23765 Z= 0.328 Chirality : 0.047 0.144 2128 Planarity : 0.005 0.051 2912 Dihedral : 17.919 89.977 2303 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.20), residues: 1792 helix: -1.68 (0.28), residues: 280 sheet: -0.99 (0.54), residues: 70 loop : -1.37 (0.17), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 109 TYR 0.016 0.002 TYR D 133 PHE 0.012 0.001 PHE G 34 TRP 0.019 0.001 TRP D 279 HIS 0.006 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00530 (16772) covalent geometry : angle 0.84725 (23765) hydrogen bonds : bond 0.02764 ( 154) hydrogen bonds : angle 6.35345 ( 441) Misc. bond : bond 0.12751 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 0.514 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: 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: B 51 LEU cc_start: 0.7419 (mt) cc_final: 0.7213 (mt) REVERT: B 54 HIS cc_start: 0.7435 (m-70) cc_final: 0.7204 (m-70) REVERT: B 60 LEU cc_start: 0.9079 (mm) cc_final: 0.8829 (pp) REVERT: B 63 GLN cc_start: 0.8810 (mt0) cc_final: 0.8396 (mt0) REVERT: B 79 ASN cc_start: 0.7911 (t0) cc_final: 0.7485 (t0) REVERT: B 95 MET cc_start: 0.8729 (mmm) cc_final: 0.8344 (mmp) REVERT: B 129 LYS cc_start: 0.9294 (ptpp) cc_final: 0.9043 (mttp) REVERT: B 203 GLN cc_start: 0.9049 (tp40) cc_final: 0.8716 (tp40) REVERT: B 204 ASP cc_start: 0.8804 (m-30) cc_final: 0.8403 (m-30) REVERT: B 238 LEU cc_start: 0.9127 (mp) cc_final: 0.8893 (mp) REVERT: B 243 LYS cc_start: 0.8669 (tmtt) cc_final: 0.8340 (tptp) REVERT: B 263 TRP cc_start: 0.8425 (m100) cc_final: 0.7927 (m100) REVERT: C 46 THR cc_start: 0.7959 (t) cc_final: 0.7463 (p) REVERT: C 51 LEU cc_start: 0.7185 (mt) cc_final: 0.6983 (mt) REVERT: C 79 ASN cc_start: 0.7869 (t0) cc_final: 0.7544 (t0) REVERT: C 90 THR cc_start: 0.8459 (p) cc_final: 0.8214 (t) REVERT: C 95 MET cc_start: 0.8449 (mmm) cc_final: 0.8124 (mmm) REVERT: C 108 PHE cc_start: 0.8944 (p90) cc_final: 0.8525 (p90) REVERT: C 109 ARG cc_start: 0.8977 (mmt180) cc_final: 0.8623 (mmt180) REVERT: C 141 ASN cc_start: 0.8702 (t0) cc_final: 0.8366 (t0) REVERT: C 179 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7266 (mt-10) REVERT: C 182 HIS cc_start: 0.8213 (m-70) cc_final: 0.7417 (m-70) REVERT: C 183 GLN cc_start: 0.6205 (pm20) cc_final: 0.5602 (pm20) REVERT: C 203 GLN cc_start: 0.9002 (tp40) cc_final: 0.8123 (tp40) REVERT: C 204 ASP cc_start: 0.8729 (m-30) cc_final: 0.8432 (m-30) REVERT: C 227 ARG cc_start: 0.8762 (mtt180) cc_final: 0.8205 (mtt180) REVERT: C 230 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7611 (mt-10) REVERT: C 243 LYS cc_start: 0.8692 (tmtt) cc_final: 0.8381 (tptp) REVERT: C 260 ASP cc_start: 0.7958 (t0) cc_final: 0.7682 (t0) REVERT: C 261 LEU cc_start: 0.8000 (pt) cc_final: 0.7721 (pt) REVERT: C 263 TRP cc_start: 0.8319 (m100) cc_final: 0.7724 (m100) REVERT: C 269 ASN cc_start: 0.7376 (m-40) cc_final: 0.7142 (m-40) REVERT: C 279 TRP cc_start: 0.7779 (t-100) cc_final: 0.7492 (t-100) REVERT: D 51 LEU cc_start: 0.7376 (mt) cc_final: 0.7150 (mt) REVERT: D 79 ASN cc_start: 0.7881 (t0) cc_final: 0.7565 (t0) REVERT: D 108 PHE cc_start: 0.8927 (p90) cc_final: 0.8452 (p90) REVERT: D 140 ASP cc_start: 0.8196 (m-30) cc_final: 0.7872 (t70) REVERT: D 141 ASN cc_start: 0.8792 (t0) cc_final: 0.8575 (t0) REVERT: D 146 HIS cc_start: 0.7823 (p-80) cc_final: 0.7622 (p90) REVERT: D 179 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7254 (mt-10) REVERT: D 203 GLN cc_start: 0.9056 (tp40) cc_final: 0.8421 (tp40) REVERT: D 204 ASP cc_start: 0.8817 (m-30) cc_final: 0.8473 (m-30) REVERT: D 213 ASP cc_start: 0.8572 (t0) cc_final: 0.8330 (t0) REVERT: D 226 ILE cc_start: 0.9085 (tp) cc_final: 0.8845 (tp) REVERT: D 230 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7635 (mt-10) REVERT: D 242 GLN cc_start: 0.8067 (tp40) cc_final: 0.7766 (tp-100) REVERT: D 269 ASN cc_start: 0.7756 (m-40) cc_final: 0.7271 (m-40) REVERT: D 279 TRP cc_start: 0.7938 (t60) cc_final: 0.7709 (t-100) REVERT: A 108 PHE cc_start: 0.8923 (p90) cc_final: 0.8691 (p90) REVERT: A 129 LYS cc_start: 0.9300 (ptpp) cc_final: 0.8954 (mtmm) REVERT: A 133 TYR cc_start: 0.8695 (t80) cc_final: 0.8389 (t80) REVERT: A 176 GLN cc_start: 0.7614 (tm-30) cc_final: 0.7300 (tm-30) REVERT: A 203 GLN cc_start: 0.8933 (tp40) cc_final: 0.8546 (tp40) REVERT: A 227 ARG cc_start: 0.8694 (mtt180) cc_final: 0.8287 (mtt180) REVERT: A 230 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7263 (mt-10) REVERT: A 260 ASP cc_start: 0.7880 (t0) cc_final: 0.7492 (t0) REVERT: A 261 LEU cc_start: 0.8224 (pt) cc_final: 0.7796 (pt) REVERT: A 269 ASN cc_start: 0.7552 (m-40) cc_final: 0.6986 (m-40) REVERT: E 51 LEU cc_start: 0.7613 (mt) cc_final: 0.7383 (mt) REVERT: E 61 VAL cc_start: 0.9303 (m) cc_final: 0.9088 (p) REVERT: E 63 GLN cc_start: 0.8814 (mt0) cc_final: 0.8476 (mt0) REVERT: E 79 ASN cc_start: 0.8020 (t0) cc_final: 0.7433 (t0) REVERT: E 95 MET cc_start: 0.8834 (mmm) cc_final: 0.8594 (mmm) REVERT: E 129 LYS cc_start: 0.9146 (mttp) cc_final: 0.8870 (tppt) REVERT: E 133 TYR cc_start: 0.8810 (t80) cc_final: 0.8459 (t80) REVERT: E 135 HIS cc_start: 0.7827 (p-80) cc_final: 0.7390 (p-80) REVERT: E 176 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7531 (tm-30) REVERT: E 203 GLN cc_start: 0.8992 (tp40) cc_final: 0.8496 (tp40) REVERT: E 204 ASP cc_start: 0.8626 (m-30) cc_final: 0.8300 (m-30) REVERT: E 269 ASN cc_start: 0.7671 (m-40) cc_final: 0.7209 (m-40) REVERT: F 51 LEU cc_start: 0.7520 (mt) cc_final: 0.7313 (mt) REVERT: F 54 HIS cc_start: 0.7671 (m-70) cc_final: 0.7367 (m-70) REVERT: F 79 ASN cc_start: 0.7681 (t0) cc_final: 0.7335 (t0) REVERT: F 95 MET cc_start: 0.8716 (mmp) cc_final: 0.8155 (mmp) REVERT: F 108 PHE cc_start: 0.8879 (p90) cc_final: 0.8533 (p90) REVERT: F 116 THR cc_start: 0.8964 (t) cc_final: 0.8711 (t) REVERT: F 176 GLN cc_start: 0.7654 (tm-30) cc_final: 0.7363 (tm-30) REVERT: F 203 GLN cc_start: 0.8966 (tp40) cc_final: 0.8170 (tp40) REVERT: F 204 ASP cc_start: 0.8878 (m-30) cc_final: 0.8360 (m-30) REVERT: F 226 ILE cc_start: 0.9039 (tp) cc_final: 0.8805 (tp) REVERT: F 230 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7646 (mt-10) REVERT: F 243 LYS cc_start: 0.8767 (tmtt) cc_final: 0.8449 (tptp) REVERT: F 263 TRP cc_start: 0.8487 (m100) cc_final: 0.7921 (m100) REVERT: F 269 ASN cc_start: 0.8051 (m-40) cc_final: 0.7065 (m-40) REVERT: G 46 THR cc_start: 0.8130 (t) cc_final: 0.7673 (p) REVERT: G 79 ASN cc_start: 0.7965 (t0) cc_final: 0.7641 (t0) REVERT: G 116 THR cc_start: 0.8831 (t) cc_final: 0.8389 (t) REVERT: G 117 GLN cc_start: 0.8356 (mm110) cc_final: 0.8113 (mm110) REVERT: G 135 HIS cc_start: 0.7443 (p90) cc_final: 0.7152 (p-80) REVERT: G 140 ASP cc_start: 0.8091 (m-30) cc_final: 0.7712 (t0) REVERT: G 141 ASN cc_start: 0.8736 (t0) cc_final: 0.8478 (t0) REVERT: G 144 ASP cc_start: 0.8117 (p0) cc_final: 0.7713 (p0) REVERT: G 146 HIS cc_start: 0.8299 (p90) cc_final: 0.7965 (p90) REVERT: G 179 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7304 (mt-10) REVERT: G 183 GLN cc_start: 0.5286 (pm20) cc_final: 0.4926 (pm20) REVERT: G 204 ASP cc_start: 0.8874 (m-30) cc_final: 0.8482 (m-30) REVERT: G 227 ARG cc_start: 0.8943 (mtt180) cc_final: 0.8261 (mtt180) REVERT: G 230 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7690 (mt-10) REVERT: G 231 VAL cc_start: 0.8702 (t) cc_final: 0.8483 (p) REVERT: G 241 ILE cc_start: 0.8857 (pt) cc_final: 0.8480 (pt) REVERT: G 242 GLN cc_start: 0.7996 (tp40) cc_final: 0.7529 (tp-100) REVERT: G 244 ASP cc_start: 0.8151 (t0) cc_final: 0.7812 (t0) REVERT: G 260 ASP cc_start: 0.8008 (t0) cc_final: 0.7658 (t0) REVERT: G 261 LEU cc_start: 0.7997 (pt) cc_final: 0.7607 (pt) REVERT: G 263 TRP cc_start: 0.8222 (m100) cc_final: 0.7731 (m100) REVERT: G 269 ASN cc_start: 0.7495 (m-40) cc_final: 0.6963 (m-40) outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.1311 time to fit residues: 86.2937 Evaluate side-chains 401 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 8 optimal weight: 0.1980 chunk 154 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 116 optimal weight: 0.0060 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 14 optimal weight: 0.0000 overall best weight: 0.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN B 135 HIS ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN B 273 GLN C 63 GLN ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN C 273 GLN D 64 HIS D 228 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN A 146 HIS A 228 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN E 228 GLN F 63 GLN F 228 GLN F 242 GLN F 273 GLN G 63 GLN ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.089103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.073636 restraints weight = 44354.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.076764 restraints weight = 24839.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.078942 restraints weight = 16185.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.080525 restraints weight = 11619.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.081680 restraints weight = 8913.651| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.360 16952 Z= 0.145 Angle : 0.823 10.744 23765 Z= 0.320 Chirality : 0.046 0.145 2128 Planarity : 0.005 0.047 2912 Dihedral : 17.759 89.330 2303 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.00 % Favored : 87.00 % Rotamer: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.20), residues: 1792 helix: -1.70 (0.27), residues: 287 sheet: None (None), residues: 0 loop : -1.24 (0.17), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 197 TYR 0.009 0.002 TYR F 133 PHE 0.012 0.001 PHE D 103 TRP 0.018 0.001 TRP E 279 HIS 0.007 0.001 HIS D 64 Details of bonding type rmsd covalent geometry : bond 0.00404 (16772) covalent geometry : angle 0.82285 (23765) hydrogen bonds : bond 0.02647 ( 154) hydrogen bonds : angle 6.31272 ( 441) Misc. bond : bond 0.09426 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 440 time to evaluate : 0.560 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: 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: B 51 LEU cc_start: 0.7313 (mt) cc_final: 0.7083 (mt) REVERT: B 63 GLN cc_start: 0.8849 (mt0) cc_final: 0.8436 (mt0) REVERT: B 79 ASN cc_start: 0.7872 (t0) cc_final: 0.7467 (t0) REVERT: B 95 MET cc_start: 0.8684 (mmm) cc_final: 0.8377 (mmp) REVERT: B 108 PHE cc_start: 0.8889 (p90) cc_final: 0.8601 (p90) REVERT: B 129 LYS cc_start: 0.9253 (ptpp) cc_final: 0.9048 (mttp) REVERT: B 135 HIS cc_start: 0.7458 (p90) cc_final: 0.7228 (p-80) REVERT: B 203 GLN cc_start: 0.9030 (tp40) cc_final: 0.8671 (tp40) REVERT: B 204 ASP cc_start: 0.8739 (m-30) cc_final: 0.8357 (m-30) REVERT: B 238 LEU cc_start: 0.9118 (mp) cc_final: 0.8894 (mp) REVERT: B 263 TRP cc_start: 0.8289 (m100) cc_final: 0.7589 (m100) REVERT: B 277 TRP cc_start: 0.8502 (t-100) cc_final: 0.8176 (t-100) REVERT: C 79 ASN cc_start: 0.7789 (t0) cc_final: 0.7448 (t0) REVERT: C 90 THR cc_start: 0.8493 (p) cc_final: 0.8232 (t) REVERT: C 108 PHE cc_start: 0.8940 (p90) cc_final: 0.8407 (p90) REVERT: C 109 ARG cc_start: 0.9033 (mmt180) cc_final: 0.8804 (mmt180) REVERT: C 117 GLN cc_start: 0.8250 (mm110) cc_final: 0.8007 (mm110) REVERT: C 129 LYS cc_start: 0.9204 (mttm) cc_final: 0.8694 (tppt) REVERT: C 135 HIS cc_start: 0.7360 (p90) cc_final: 0.6929 (p-80) REVERT: C 179 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7046 (mt-10) REVERT: C 182 HIS cc_start: 0.8115 (m-70) cc_final: 0.7236 (m170) REVERT: C 183 GLN cc_start: 0.5942 (pm20) cc_final: 0.5518 (pm20) REVERT: C 203 GLN cc_start: 0.8982 (tp40) cc_final: 0.8099 (tp40) REVERT: C 204 ASP cc_start: 0.8677 (m-30) cc_final: 0.8349 (m-30) REVERT: C 216 LEU cc_start: 0.9036 (tt) cc_final: 0.8202 (mt) REVERT: C 269 ASN cc_start: 0.7443 (m-40) cc_final: 0.6749 (m-40) REVERT: C 279 TRP cc_start: 0.7694 (t-100) cc_final: 0.7441 (t-100) REVERT: D 51 LEU cc_start: 0.7307 (mt) cc_final: 0.7088 (mt) REVERT: D 79 ASN cc_start: 0.7801 (t0) cc_final: 0.7440 (t0) REVERT: D 108 PHE cc_start: 0.8890 (p90) cc_final: 0.8555 (p90) REVERT: D 129 LYS cc_start: 0.9275 (mttp) cc_final: 0.9075 (mmtm) REVERT: D 133 TYR cc_start: 0.8618 (t80) cc_final: 0.8417 (t80) REVERT: D 179 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7081 (mt-10) REVERT: D 183 GLN cc_start: 0.7149 (pm20) cc_final: 0.6501 (pm20) REVERT: D 203 GLN cc_start: 0.9013 (tp40) cc_final: 0.8381 (tp40) REVERT: D 204 ASP cc_start: 0.8789 (m-30) cc_final: 0.8439 (m-30) REVERT: D 213 ASP cc_start: 0.8590 (t0) cc_final: 0.8322 (t0) REVERT: D 226 ILE cc_start: 0.9061 (tp) cc_final: 0.8826 (tp) REVERT: D 227 ARG cc_start: 0.8813 (mtt180) cc_final: 0.8372 (mtt180) REVERT: D 230 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7565 (mt-10) REVERT: D 242 GLN cc_start: 0.8138 (tp40) cc_final: 0.7822 (tp-100) REVERT: D 260 ASP cc_start: 0.7920 (t0) cc_final: 0.7599 (t0) REVERT: D 261 LEU cc_start: 0.8287 (pt) cc_final: 0.7838 (pt) REVERT: D 269 ASN cc_start: 0.7679 (m-40) cc_final: 0.7162 (m-40) REVERT: D 279 TRP cc_start: 0.7914 (t60) cc_final: 0.7700 (t-100) REVERT: A 129 LYS cc_start: 0.9289 (ptpp) cc_final: 0.8964 (mtmm) REVERT: A 133 TYR cc_start: 0.8621 (t80) cc_final: 0.8345 (t80) REVERT: A 176 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7262 (tm-30) REVERT: A 203 GLN cc_start: 0.8676 (tp40) cc_final: 0.8301 (tp40) REVERT: A 226 ILE cc_start: 0.9063 (tp) cc_final: 0.8761 (tp) REVERT: A 227 ARG cc_start: 0.8670 (mtt180) cc_final: 0.8265 (mtt180) REVERT: A 228 GLN cc_start: 0.8554 (tt0) cc_final: 0.8138 (tm-30) REVERT: A 230 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7166 (mt-10) REVERT: A 260 ASP cc_start: 0.7848 (t0) cc_final: 0.7621 (t0) REVERT: A 261 LEU cc_start: 0.8158 (pt) cc_final: 0.7833 (pt) REVERT: A 269 ASN cc_start: 0.7406 (m-40) cc_final: 0.7067 (m-40) REVERT: E 51 LEU cc_start: 0.7487 (mt) cc_final: 0.7284 (mt) REVERT: E 60 LEU cc_start: 0.8912 (mm) cc_final: 0.8691 (pp) REVERT: E 61 VAL cc_start: 0.9258 (m) cc_final: 0.9032 (p) REVERT: E 63 GLN cc_start: 0.8725 (mt0) cc_final: 0.8402 (mt0) REVERT: E 79 ASN cc_start: 0.7993 (t0) cc_final: 0.7530 (t0) REVERT: E 129 LYS cc_start: 0.9126 (mttp) cc_final: 0.8754 (tppt) REVERT: E 133 TYR cc_start: 0.8731 (t80) cc_final: 0.8397 (t80) REVERT: E 135 HIS cc_start: 0.7827 (p-80) cc_final: 0.7328 (p-80) REVERT: E 139 ILE cc_start: 0.8907 (tp) cc_final: 0.8704 (tp) REVERT: E 148 ILE cc_start: 0.9061 (mm) cc_final: 0.8841 (mm) REVERT: E 176 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7518 (tm-30) REVERT: E 203 GLN cc_start: 0.8964 (tp40) cc_final: 0.8472 (tp40) REVERT: E 204 ASP cc_start: 0.8633 (m-30) cc_final: 0.8340 (m-30) REVERT: E 213 ASP cc_start: 0.8541 (t0) cc_final: 0.8216 (t0) REVERT: E 228 GLN cc_start: 0.8314 (tt0) cc_final: 0.8075 (tm-30) REVERT: E 260 ASP cc_start: 0.7980 (t0) cc_final: 0.7716 (t0) REVERT: E 261 LEU cc_start: 0.8121 (pt) cc_final: 0.7838 (pt) REVERT: E 269 ASN cc_start: 0.8135 (m-40) cc_final: 0.7168 (m-40) REVERT: F 51 LEU cc_start: 0.7394 (mt) cc_final: 0.7162 (mt) REVERT: F 79 ASN cc_start: 0.7627 (t0) cc_final: 0.7259 (t0) REVERT: F 95 MET cc_start: 0.8631 (mmp) cc_final: 0.8132 (mmp) REVERT: F 108 PHE cc_start: 0.8930 (p90) cc_final: 0.8724 (p90) REVERT: F 116 THR cc_start: 0.8970 (t) cc_final: 0.8724 (t) REVERT: F 129 LYS cc_start: 0.9206 (mttp) cc_final: 0.8733 (tppt) REVERT: F 135 HIS cc_start: 0.7354 (p90) cc_final: 0.7077 (p90) REVERT: F 203 GLN cc_start: 0.8986 (tp40) cc_final: 0.8231 (tp40) REVERT: F 204 ASP cc_start: 0.8854 (m-30) cc_final: 0.8423 (m-30) REVERT: F 216 LEU cc_start: 0.8985 (tt) cc_final: 0.8297 (mt) REVERT: F 230 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7535 (mt-10) REVERT: F 238 LEU cc_start: 0.9026 (mt) cc_final: 0.8823 (mt) REVERT: F 243 LYS cc_start: 0.8735 (tmtt) cc_final: 0.8418 (tptp) REVERT: F 263 TRP cc_start: 0.8425 (m100) cc_final: 0.7803 (m100) REVERT: F 269 ASN cc_start: 0.7482 (m-40) cc_final: 0.6760 (m-40) REVERT: G 46 THR cc_start: 0.8030 (t) cc_final: 0.7574 (p) REVERT: G 79 ASN cc_start: 0.7960 (t0) cc_final: 0.7585 (t0) REVERT: G 116 THR cc_start: 0.8794 (t) cc_final: 0.8457 (t) REVERT: G 117 GLN cc_start: 0.8363 (mm110) cc_final: 0.8160 (mm110) REVERT: G 129 LYS cc_start: 0.9229 (ptpp) cc_final: 0.8892 (mttp) REVERT: G 179 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7138 (mt-10) REVERT: G 203 GLN cc_start: 0.9077 (tp40) cc_final: 0.8135 (tp40) REVERT: G 204 ASP cc_start: 0.8826 (m-30) cc_final: 0.8499 (m-30) REVERT: G 226 ILE cc_start: 0.8914 (tp) cc_final: 0.8654 (tp) REVERT: G 227 ARG cc_start: 0.8756 (mtt180) cc_final: 0.8145 (mtt180) REVERT: G 228 GLN cc_start: 0.8463 (tt0) cc_final: 0.7587 (tm-30) REVERT: G 230 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7590 (mt-10) REVERT: G 241 ILE cc_start: 0.8872 (pt) cc_final: 0.8567 (pt) REVERT: G 242 GLN cc_start: 0.8046 (tp40) cc_final: 0.7782 (tp40) REVERT: G 263 TRP cc_start: 0.8159 (m100) cc_final: 0.7798 (m100) REVERT: G 269 ASN cc_start: 0.7484 (m-40) cc_final: 0.6864 (m-40) outliers start: 1 outliers final: 0 residues processed: 440 average time/residue: 0.1308 time to fit residues: 83.9762 Evaluate side-chains 403 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 16 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 97 optimal weight: 0.0670 chunk 141 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN B 228 GLN B 273 GLN C 228 GLN C 273 GLN ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN D 273 GLN ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS A 228 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN E 228 GLN F 63 GLN F 228 GLN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 HIS ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.083975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.068849 restraints weight = 46536.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.071699 restraints weight = 27215.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.073693 restraints weight = 18272.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.075165 restraints weight = 13421.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.076199 restraints weight = 10485.597| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.543 16952 Z= 0.255 Angle : 0.923 10.651 23765 Z= 0.354 Chirality : 0.049 0.148 2128 Planarity : 0.005 0.044 2912 Dihedral : 18.094 89.978 2303 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.34 % Favored : 85.66 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.20), residues: 1792 helix: -1.84 (0.27), residues: 287 sheet: -1.61 (0.56), residues: 70 loop : -1.38 (0.18), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 197 TYR 0.014 0.002 TYR B 151 PHE 0.018 0.002 PHE E 34 TRP 0.024 0.002 TRP F 279 HIS 0.009 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00732 (16772) covalent geometry : angle 0.92253 (23765) hydrogen bonds : bond 0.03192 ( 154) hydrogen bonds : angle 6.64273 ( 441) Misc. bond : bond 0.17136 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 0.417 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: 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: B 51 LEU cc_start: 0.7507 (mt) cc_final: 0.7305 (mt) REVERT: B 63 GLN cc_start: 0.8894 (mt0) cc_final: 0.8514 (mt0) REVERT: B 79 ASN cc_start: 0.8101 (t0) cc_final: 0.7805 (t0) REVERT: B 95 MET cc_start: 0.8727 (mmm) cc_final: 0.8346 (mmm) REVERT: B 129 LYS cc_start: 0.9265 (ptpp) cc_final: 0.9060 (mttp) REVERT: B 183 GLN cc_start: 0.7469 (pm20) cc_final: 0.7232 (pm20) REVERT: B 203 GLN cc_start: 0.9074 (tp40) cc_final: 0.8453 (tp40) REVERT: B 204 ASP cc_start: 0.8863 (m-30) cc_final: 0.8464 (m-30) REVERT: B 227 ARG cc_start: 0.9154 (mtt180) cc_final: 0.8605 (mtt180) REVERT: B 228 GLN cc_start: 0.8489 (tt0) cc_final: 0.8010 (tm-30) REVERT: B 230 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7740 (mt-10) REVERT: B 238 LEU cc_start: 0.9111 (mp) cc_final: 0.8874 (mp) REVERT: C 51 LEU cc_start: 0.7513 (mt) cc_final: 0.7263 (mt) REVERT: C 90 THR cc_start: 0.8474 (p) cc_final: 0.8250 (t) REVERT: C 95 MET cc_start: 0.8634 (mmp) cc_final: 0.8327 (mmp) REVERT: C 108 PHE cc_start: 0.8987 (p90) cc_final: 0.8418 (p90) REVERT: C 109 ARG cc_start: 0.9122 (mmt180) cc_final: 0.8675 (mmt180) REVERT: C 117 GLN cc_start: 0.8284 (mm110) cc_final: 0.8064 (mm-40) REVERT: C 129 LYS cc_start: 0.9234 (mttm) cc_final: 0.9008 (tppt) REVERT: C 135 HIS cc_start: 0.7316 (p90) cc_final: 0.7026 (p90) REVERT: C 139 ILE cc_start: 0.8732 (tp) cc_final: 0.8484 (tp) REVERT: C 149 PRO cc_start: 0.8786 (Cg_exo) cc_final: 0.8303 (Cg_endo) REVERT: C 179 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7527 (mt-10) REVERT: C 182 HIS cc_start: 0.8361 (m-70) cc_final: 0.7570 (m-70) REVERT: C 183 GLN cc_start: 0.5887 (pm20) cc_final: 0.5611 (pm20) REVERT: C 203 GLN cc_start: 0.8839 (tp40) cc_final: 0.7772 (tp40) REVERT: C 204 ASP cc_start: 0.8779 (m-30) cc_final: 0.8484 (m-30) REVERT: C 230 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7608 (mt-10) REVERT: C 236 ASN cc_start: 0.8495 (p0) cc_final: 0.8273 (t0) REVERT: C 238 LEU cc_start: 0.8939 (mt) cc_final: 0.8717 (mt) REVERT: C 243 LYS cc_start: 0.8938 (tptp) cc_final: 0.8626 (tptp) REVERT: C 269 ASN cc_start: 0.7646 (m-40) cc_final: 0.7347 (m-40) REVERT: C 279 TRP cc_start: 0.7741 (t-100) cc_final: 0.7500 (t-100) REVERT: D 46 THR cc_start: 0.8274 (t) cc_final: 0.7908 (t) REVERT: D 51 LEU cc_start: 0.7553 (mt) cc_final: 0.7307 (mt) REVERT: D 63 GLN cc_start: 0.8452 (pm20) cc_final: 0.8172 (pm20) REVERT: D 108 PHE cc_start: 0.8956 (p90) cc_final: 0.8450 (p90) REVERT: D 129 LYS cc_start: 0.9276 (mttp) cc_final: 0.8954 (mmtm) REVERT: D 176 GLN cc_start: 0.7324 (tm-30) cc_final: 0.7106 (tm-30) REVERT: D 203 GLN cc_start: 0.8888 (tp40) cc_final: 0.8214 (tp40) REVERT: D 204 ASP cc_start: 0.8879 (m-30) cc_final: 0.8530 (m-30) REVERT: D 213 ASP cc_start: 0.8657 (t0) cc_final: 0.8368 (t0) REVERT: D 226 ILE cc_start: 0.9112 (tp) cc_final: 0.8903 (tp) REVERT: D 230 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7672 (mt-10) REVERT: D 238 LEU cc_start: 0.8980 (mt) cc_final: 0.8755 (mt) REVERT: D 242 GLN cc_start: 0.8142 (tp40) cc_final: 0.7813 (tp-100) REVERT: D 260 ASP cc_start: 0.8060 (t0) cc_final: 0.7823 (t0) REVERT: D 261 LEU cc_start: 0.8476 (pt) cc_final: 0.8118 (pt) REVERT: D 269 ASN cc_start: 0.7758 (m-40) cc_final: 0.7133 (m-40) REVERT: D 279 TRP cc_start: 0.7998 (t60) cc_final: 0.7710 (t-100) REVERT: A 34 PHE cc_start: 0.8768 (p90) cc_final: 0.8545 (p90) REVERT: A 46 THR cc_start: 0.8382 (t) cc_final: 0.8017 (t) REVERT: A 51 LEU cc_start: 0.7643 (mt) cc_final: 0.7391 (mt) REVERT: A 90 THR cc_start: 0.8577 (p) cc_final: 0.8363 (t) REVERT: A 95 MET cc_start: 0.8856 (mmp) cc_final: 0.8639 (mmm) REVERT: A 129 LYS cc_start: 0.9282 (ptpp) cc_final: 0.8972 (mtmm) REVERT: A 133 TYR cc_start: 0.8749 (t80) cc_final: 0.8409 (t80) REVERT: A 176 GLN cc_start: 0.7352 (tm-30) cc_final: 0.6999 (tm-30) REVERT: A 203 GLN cc_start: 0.8843 (tp40) cc_final: 0.8331 (tp40) REVERT: A 204 ASP cc_start: 0.8896 (m-30) cc_final: 0.8618 (m-30) REVERT: A 227 ARG cc_start: 0.8805 (mtt180) cc_final: 0.8363 (mtt180) REVERT: A 230 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7362 (mt-10) REVERT: A 260 ASP cc_start: 0.7979 (t0) cc_final: 0.7695 (t0) REVERT: A 261 LEU cc_start: 0.8312 (pt) cc_final: 0.7964 (pt) REVERT: A 269 ASN cc_start: 0.7723 (m-40) cc_final: 0.7231 (m-40) REVERT: E 46 THR cc_start: 0.8278 (t) cc_final: 0.7744 (p) REVERT: E 51 LEU cc_start: 0.7745 (mt) cc_final: 0.7520 (mt) REVERT: E 54 HIS cc_start: 0.7478 (m-70) cc_final: 0.7242 (m-70) REVERT: E 61 VAL cc_start: 0.9323 (m) cc_final: 0.9109 (p) REVERT: E 63 GLN cc_start: 0.8818 (mt0) cc_final: 0.8448 (mt0) REVERT: E 79 ASN cc_start: 0.8064 (t0) cc_final: 0.7706 (t0) REVERT: E 108 PHE cc_start: 0.9000 (p90) cc_final: 0.8505 (p90) REVERT: E 109 ARG cc_start: 0.8906 (mmt90) cc_final: 0.8609 (mmt90) REVERT: E 129 LYS cc_start: 0.9106 (mttp) cc_final: 0.8812 (mmtp) REVERT: E 133 TYR cc_start: 0.8805 (t80) cc_final: 0.8466 (t80) REVERT: E 135 HIS cc_start: 0.7973 (p-80) cc_final: 0.7576 (p-80) REVERT: E 203 GLN cc_start: 0.9016 (tp40) cc_final: 0.8393 (tp40) REVERT: E 204 ASP cc_start: 0.8778 (m-30) cc_final: 0.8451 (m-30) REVERT: E 227 ARG cc_start: 0.8940 (mtt180) cc_final: 0.8532 (mtt180) REVERT: E 230 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7566 (mt-10) REVERT: E 269 ASN cc_start: 0.7974 (m-40) cc_final: 0.7390 (m-40) REVERT: F 51 LEU cc_start: 0.7655 (mt) cc_final: 0.7428 (mt) REVERT: F 79 ASN cc_start: 0.7886 (t0) cc_final: 0.7545 (t0) REVERT: F 95 MET cc_start: 0.8589 (mmp) cc_final: 0.8099 (mmp) REVERT: F 108 PHE cc_start: 0.9050 (p90) cc_final: 0.8701 (p90) REVERT: F 129 LYS cc_start: 0.9208 (mttp) cc_final: 0.8930 (tppt) REVERT: F 130 ASP cc_start: 0.8090 (t0) cc_final: 0.7835 (t0) REVERT: F 183 GLN cc_start: 0.6940 (pm20) cc_final: 0.6708 (pm20) REVERT: F 203 GLN cc_start: 0.9078 (tp40) cc_final: 0.8109 (tp40) REVERT: F 204 ASP cc_start: 0.8953 (m-30) cc_final: 0.8524 (m-30) REVERT: F 226 ILE cc_start: 0.9109 (tp) cc_final: 0.8838 (tp) REVERT: F 227 ARG cc_start: 0.8818 (mtt180) cc_final: 0.8168 (mtt180) REVERT: F 228 GLN cc_start: 0.8651 (tt0) cc_final: 0.8215 (tm-30) REVERT: F 230 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7592 (mt-10) REVERT: F 243 LYS cc_start: 0.8811 (tmtt) cc_final: 0.8523 (tptp) REVERT: F 263 TRP cc_start: 0.8503 (m100) cc_final: 0.8009 (m100) REVERT: F 269 ASN cc_start: 0.8190 (m-40) cc_final: 0.7323 (m-40) REVERT: G 79 ASN cc_start: 0.8097 (t0) cc_final: 0.7803 (t0) REVERT: G 108 PHE cc_start: 0.9185 (p90) cc_final: 0.8724 (p90) REVERT: G 116 THR cc_start: 0.8820 (t) cc_final: 0.8373 (t) REVERT: G 117 GLN cc_start: 0.8315 (mm110) cc_final: 0.8014 (mm110) REVERT: G 140 ASP cc_start: 0.8131 (m-30) cc_final: 0.7785 (t0) REVERT: G 141 ASN cc_start: 0.8702 (t0) cc_final: 0.8419 (t0) REVERT: G 149 PRO cc_start: 0.8884 (Cg_exo) cc_final: 0.8576 (Cg_endo) REVERT: G 179 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7447 (mt-10) REVERT: G 182 HIS cc_start: 0.8221 (m-70) cc_final: 0.7250 (m170) REVERT: G 204 ASP cc_start: 0.8902 (m-30) cc_final: 0.8583 (m-30) REVERT: G 227 ARG cc_start: 0.8830 (mtt180) cc_final: 0.8183 (mtt180) REVERT: G 230 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7714 (mt-10) REVERT: G 241 ILE cc_start: 0.8918 (pt) cc_final: 0.8319 (pt) REVERT: G 242 GLN cc_start: 0.7984 (tp40) cc_final: 0.7455 (tp-100) REVERT: G 244 ASP cc_start: 0.8061 (t0) cc_final: 0.7790 (t0) REVERT: G 263 TRP cc_start: 0.8330 (m100) cc_final: 0.7884 (m100) REVERT: G 266 ILE cc_start: 0.8602 (mp) cc_final: 0.8266 (mp) REVERT: G 269 ASN cc_start: 0.7578 (m-40) cc_final: 0.7067 (m-40) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 0.1314 time to fit residues: 87.6661 Evaluate side-chains 424 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 22 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 158 optimal weight: 0.0970 chunk 122 optimal weight: 0.8980 chunk 162 optimal weight: 0.0470 chunk 111 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN B 228 GLN C 63 GLN C 228 GLN D 64 HIS D 117 GLN D 135 HIS D 228 GLN A 117 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS A 228 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN F 228 GLN F 273 GLN G 63 GLN G 135 HIS G 146 HIS G 228 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.086890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.071700 restraints weight = 45354.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.074735 restraints weight = 25480.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.076838 restraints weight = 16652.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.078343 restraints weight = 12006.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.079464 restraints weight = 9262.876| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.392 16952 Z= 0.166 Angle : 0.853 10.385 23765 Z= 0.331 Chirality : 0.047 0.148 2128 Planarity : 0.004 0.042 2912 Dihedral : 17.967 89.631 2303 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.20), residues: 1792 helix: -1.90 (0.27), residues: 287 sheet: -1.56 (0.59), residues: 70 loop : -1.42 (0.18), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 197 TYR 0.009 0.001 TYR B 151 PHE 0.013 0.001 PHE E 103 TRP 0.022 0.002 TRP F 279 HIS 0.008 0.001 HIS D 64 Details of bonding type rmsd covalent geometry : bond 0.00454 (16772) covalent geometry : angle 0.85339 (23765) hydrogen bonds : bond 0.02908 ( 154) hydrogen bonds : angle 6.53702 ( 441) Misc. bond : bond 0.11972 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 0.517 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: 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: B 63 GLN cc_start: 0.8868 (mt0) cc_final: 0.8374 (mp10) REVERT: B 95 MET cc_start: 0.8668 (mmm) cc_final: 0.8370 (mmp) REVERT: B 108 PHE cc_start: 0.8929 (p90) cc_final: 0.8535 (p90) REVERT: B 176 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7291 (tm-30) REVERT: B 203 GLN cc_start: 0.9036 (tp40) cc_final: 0.8372 (tp40) REVERT: B 204 ASP cc_start: 0.8819 (m-30) cc_final: 0.8380 (m-30) REVERT: B 227 ARG cc_start: 0.9157 (mtt180) cc_final: 0.8691 (mtt180) REVERT: B 230 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7749 (mt-10) REVERT: B 238 LEU cc_start: 0.9138 (mp) cc_final: 0.8908 (mp) REVERT: B 243 LYS cc_start: 0.8973 (tptp) cc_final: 0.8732 (tptp) REVERT: B 255 LYS cc_start: 0.8784 (ptpp) cc_final: 0.8571 (ptpp) REVERT: C 46 THR cc_start: 0.8178 (t) cc_final: 0.7689 (p) REVERT: C 54 HIS cc_start: 0.7183 (m-70) cc_final: 0.6979 (m-70) REVERT: C 90 THR cc_start: 0.8504 (p) cc_final: 0.8268 (t) REVERT: C 95 MET cc_start: 0.8674 (mmp) cc_final: 0.8334 (mmp) REVERT: C 108 PHE cc_start: 0.9010 (p90) cc_final: 0.8364 (p90) REVERT: C 109 ARG cc_start: 0.9083 (mmt180) cc_final: 0.8712 (mmt180) REVERT: C 117 GLN cc_start: 0.8276 (mm110) cc_final: 0.8057 (mm-40) REVERT: C 129 LYS cc_start: 0.9205 (mttm) cc_final: 0.8968 (tppt) REVERT: C 135 HIS cc_start: 0.7380 (p90) cc_final: 0.7054 (p90) REVERT: C 139 ILE cc_start: 0.8697 (tp) cc_final: 0.8494 (tp) REVERT: C 149 PRO cc_start: 0.8752 (Cg_exo) cc_final: 0.8238 (Cg_endo) REVERT: C 179 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7364 (mt-10) REVERT: C 182 HIS cc_start: 0.8177 (m-70) cc_final: 0.7282 (m170) REVERT: C 203 GLN cc_start: 0.8759 (tp40) cc_final: 0.7735 (tp40) REVERT: C 204 ASP cc_start: 0.8687 (m-30) cc_final: 0.8380 (m-30) REVERT: C 228 GLN cc_start: 0.8348 (tt0) cc_final: 0.7970 (tm-30) REVERT: C 230 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7493 (mt-10) REVERT: C 238 LEU cc_start: 0.8932 (mt) cc_final: 0.8553 (mp) REVERT: C 243 LYS cc_start: 0.8924 (tptp) cc_final: 0.8631 (tptp) REVERT: C 269 ASN cc_start: 0.7415 (m-40) cc_final: 0.6773 (m-40) REVERT: D 51 LEU cc_start: 0.7445 (mt) cc_final: 0.7194 (mt) REVERT: D 79 ASN cc_start: 0.7886 (t0) cc_final: 0.7572 (t0) REVERT: D 108 PHE cc_start: 0.8949 (p90) cc_final: 0.8390 (p90) REVERT: D 129 LYS cc_start: 0.9183 (mttp) cc_final: 0.8912 (mmtm) REVERT: D 179 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7377 (mt-10) REVERT: D 203 GLN cc_start: 0.8790 (tp40) cc_final: 0.8107 (tp40) REVERT: D 204 ASP cc_start: 0.8831 (m-30) cc_final: 0.8499 (m-30) REVERT: D 213 ASP cc_start: 0.8635 (t0) cc_final: 0.8335 (t0) REVERT: D 226 ILE cc_start: 0.9047 (tp) cc_final: 0.8837 (tp) REVERT: D 227 ARG cc_start: 0.8704 (mtt180) cc_final: 0.8314 (mtt180) REVERT: D 230 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7459 (mt-10) REVERT: D 242 GLN cc_start: 0.8125 (tp40) cc_final: 0.7828 (tp-100) REVERT: D 260 ASP cc_start: 0.8025 (t0) cc_final: 0.7753 (t0) REVERT: D 261 LEU cc_start: 0.8395 (pt) cc_final: 0.7990 (pt) REVERT: D 269 ASN cc_start: 0.7698 (m-40) cc_final: 0.7487 (m-40) REVERT: D 279 TRP cc_start: 0.7893 (t60) cc_final: 0.7654 (t-100) REVERT: A 46 THR cc_start: 0.8411 (t) cc_final: 0.7928 (p) REVERT: A 79 ASN cc_start: 0.7596 (t0) cc_final: 0.7302 (t0) REVERT: A 90 THR cc_start: 0.8616 (p) cc_final: 0.8401 (t) REVERT: A 133 TYR cc_start: 0.8682 (t80) cc_final: 0.8346 (t80) REVERT: A 176 GLN cc_start: 0.7310 (tm-30) cc_final: 0.6817 (tm-30) REVERT: A 203 GLN cc_start: 0.8783 (tp40) cc_final: 0.8287 (tp40) REVERT: A 226 ILE cc_start: 0.8987 (tp) cc_final: 0.8595 (tp) REVERT: A 227 ARG cc_start: 0.8673 (mtt180) cc_final: 0.8266 (mtt180) REVERT: A 228 GLN cc_start: 0.8531 (tt0) cc_final: 0.8225 (tm-30) REVERT: A 230 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7191 (mt-10) REVERT: A 260 ASP cc_start: 0.8000 (t0) cc_final: 0.7603 (t0) REVERT: A 261 LEU cc_start: 0.8237 (pt) cc_final: 0.7824 (pt) REVERT: A 269 ASN cc_start: 0.7670 (m-40) cc_final: 0.7003 (m-40) REVERT: A 271 ASP cc_start: 0.7998 (p0) cc_final: 0.7753 (p0) REVERT: E 61 VAL cc_start: 0.9294 (m) cc_final: 0.9093 (p) REVERT: E 63 GLN cc_start: 0.8824 (mt0) cc_final: 0.8408 (mt0) REVERT: E 79 ASN cc_start: 0.8005 (t0) cc_final: 0.7594 (t0) REVERT: E 129 LYS cc_start: 0.9130 (mttp) cc_final: 0.8846 (mmtp) REVERT: E 133 TYR cc_start: 0.8745 (t80) cc_final: 0.8359 (t80) REVERT: E 135 HIS cc_start: 0.7978 (p-80) cc_final: 0.7594 (p-80) REVERT: E 148 ILE cc_start: 0.9106 (mm) cc_final: 0.8840 (mm) REVERT: E 182 HIS cc_start: 0.7407 (m170) cc_final: 0.7101 (m170) REVERT: E 203 GLN cc_start: 0.8999 (tp40) cc_final: 0.8340 (tp40) REVERT: E 204 ASP cc_start: 0.8751 (m-30) cc_final: 0.8402 (m-30) REVERT: E 269 ASN cc_start: 0.7784 (m-40) cc_final: 0.7113 (m-40) REVERT: F 79 ASN cc_start: 0.7775 (t0) cc_final: 0.7425 (t0) REVERT: F 95 MET cc_start: 0.8593 (mmp) cc_final: 0.8188 (mmp) REVERT: F 108 PHE cc_start: 0.8993 (p90) cc_final: 0.8706 (p90) REVERT: F 129 LYS cc_start: 0.9180 (mttp) cc_final: 0.8958 (tppt) REVERT: F 176 GLN cc_start: 0.7706 (tm-30) cc_final: 0.7098 (tm-30) REVERT: F 203 GLN cc_start: 0.9031 (tp40) cc_final: 0.8181 (tp40) REVERT: F 204 ASP cc_start: 0.8881 (m-30) cc_final: 0.8438 (m-30) REVERT: F 226 ILE cc_start: 0.9041 (tp) cc_final: 0.8785 (tp) REVERT: F 230 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7596 (mt-10) REVERT: F 243 LYS cc_start: 0.8776 (tmtt) cc_final: 0.8498 (tptp) REVERT: F 263 TRP cc_start: 0.8447 (m100) cc_final: 0.7979 (m100) REVERT: F 269 ASN cc_start: 0.7542 (m-40) cc_final: 0.6898 (m-40) REVERT: F 279 TRP cc_start: 0.7880 (t60) cc_final: 0.7429 (t-100) REVERT: G 46 THR cc_start: 0.8361 (t) cc_final: 0.7589 (p) REVERT: G 54 HIS cc_start: 0.7381 (m-70) cc_final: 0.7133 (m-70) REVERT: G 79 ASN cc_start: 0.8124 (t0) cc_final: 0.7754 (t0) REVERT: G 116 THR cc_start: 0.8815 (t) cc_final: 0.8423 (t) REVERT: G 117 GLN cc_start: 0.8314 (mm110) cc_final: 0.8015 (mm110) REVERT: G 149 PRO cc_start: 0.8852 (Cg_exo) cc_final: 0.8523 (Cg_endo) REVERT: G 179 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7189 (mt-10) REVERT: G 203 GLN cc_start: 0.8950 (tp40) cc_final: 0.8458 (tp40) REVERT: G 204 ASP cc_start: 0.8821 (m-30) cc_final: 0.8511 (m-30) REVERT: G 226 ILE cc_start: 0.8922 (tp) cc_final: 0.8665 (tp) REVERT: G 228 GLN cc_start: 0.8513 (tt0) cc_final: 0.7937 (tm-30) REVERT: G 230 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7620 (mt-10) REVERT: G 241 ILE cc_start: 0.8932 (pt) cc_final: 0.8489 (pt) REVERT: G 242 GLN cc_start: 0.8019 (tp40) cc_final: 0.7597 (tp40) REVERT: G 263 TRP cc_start: 0.8217 (m100) cc_final: 0.7882 (m100) REVERT: G 266 ILE cc_start: 0.8721 (mp) cc_final: 0.8485 (mp) REVERT: G 269 ASN cc_start: 0.7514 (m-40) cc_final: 0.6978 (m-40) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.1291 time to fit residues: 84.1725 Evaluate side-chains 420 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 HIS ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS B 228 GLN C 228 GLN D 117 GLN ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS D 228 GLN A 117 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 GLN ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 GLN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 HIS G 228 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.084377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.069493 restraints weight = 46772.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.072358 restraints weight = 27064.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.074339 restraints weight = 18073.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.075792 restraints weight = 13253.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.076846 restraints weight = 10342.574| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.510 16952 Z= 0.218 Angle : 0.908 12.264 23765 Z= 0.344 Chirality : 0.048 0.140 2128 Planarity : 0.005 0.046 2912 Dihedral : 18.165 89.834 2303 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.56 % Favored : 86.44 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.21), residues: 1792 helix: -1.94 (0.27), residues: 287 sheet: -1.96 (0.60), residues: 70 loop : -1.43 (0.18), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 197 TYR 0.014 0.002 TYR B 151 PHE 0.015 0.002 PHE G 42 TRP 0.016 0.002 TRP D 270 HIS 0.008 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00608 (16772) covalent geometry : angle 0.90834 (23765) hydrogen bonds : bond 0.03056 ( 154) hydrogen bonds : angle 6.68719 ( 441) Misc. bond : bond 0.15823 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 0.503 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: 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: B 63 GLN cc_start: 0.8921 (mt0) cc_final: 0.8414 (mp10) REVERT: B 79 ASN cc_start: 0.8051 (t0) cc_final: 0.7829 (t0) REVERT: B 95 MET cc_start: 0.8697 (mmm) cc_final: 0.8361 (mmp) REVERT: B 149 PRO cc_start: 0.9148 (Cg_exo) cc_final: 0.8901 (Cg_endo) REVERT: B 176 GLN cc_start: 0.7624 (tm-30) cc_final: 0.7248 (tm-30) REVERT: B 203 GLN cc_start: 0.8880 (tp40) cc_final: 0.8297 (tp40) REVERT: B 204 ASP cc_start: 0.8865 (m-30) cc_final: 0.8427 (m-30) REVERT: B 227 ARG cc_start: 0.9093 (mtt180) cc_final: 0.8481 (mtt180) REVERT: B 228 GLN cc_start: 0.8437 (tt0) cc_final: 0.8127 (tm-30) REVERT: B 230 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7719 (mt-10) REVERT: B 238 LEU cc_start: 0.9114 (mp) cc_final: 0.8887 (mp) REVERT: B 243 LYS cc_start: 0.9003 (tptp) cc_final: 0.8752 (tptp) REVERT: B 255 LYS cc_start: 0.8813 (ptpp) cc_final: 0.8554 (pttm) REVERT: C 54 HIS cc_start: 0.7477 (m-70) cc_final: 0.7096 (m-70) REVERT: C 90 THR cc_start: 0.8530 (p) cc_final: 0.8264 (t) REVERT: C 95 MET cc_start: 0.8631 (mmp) cc_final: 0.8360 (mmp) REVERT: C 108 PHE cc_start: 0.9047 (p90) cc_final: 0.8388 (p90) REVERT: C 109 ARG cc_start: 0.9077 (mmt180) cc_final: 0.8677 (mmt180) REVERT: C 149 PRO cc_start: 0.8770 (Cg_exo) cc_final: 0.8353 (Cg_endo) REVERT: C 182 HIS cc_start: 0.8334 (m-70) cc_final: 0.7271 (m170) REVERT: C 183 GLN cc_start: 0.6259 (pm20) cc_final: 0.5608 (pm20) REVERT: C 203 GLN cc_start: 0.8785 (tp40) cc_final: 0.7701 (tp40) REVERT: C 204 ASP cc_start: 0.8793 (m-30) cc_final: 0.8470 (m-30) REVERT: C 226 ILE cc_start: 0.8963 (tp) cc_final: 0.8600 (tp) REVERT: C 230 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7364 (mt-10) REVERT: C 238 LEU cc_start: 0.8956 (mt) cc_final: 0.8569 (mp) REVERT: C 243 LYS cc_start: 0.8952 (tptp) cc_final: 0.8538 (tptp) REVERT: C 255 LYS cc_start: 0.8678 (ptpp) cc_final: 0.8426 (ptpp) REVERT: C 263 TRP cc_start: 0.8307 (m100) cc_final: 0.7869 (m100) REVERT: C 269 ASN cc_start: 0.7499 (m-40) cc_final: 0.6948 (m-40) REVERT: D 46 THR cc_start: 0.7924 (t) cc_final: 0.7644 (t) REVERT: D 51 LEU cc_start: 0.7567 (mt) cc_final: 0.7340 (mt) REVERT: D 79 ASN cc_start: 0.7977 (t0) cc_final: 0.7708 (t0) REVERT: D 108 PHE cc_start: 0.8958 (p90) cc_final: 0.8031 (p90) REVERT: D 109 ARG cc_start: 0.9131 (mmt180) cc_final: 0.8841 (mmt180) REVERT: D 129 LYS cc_start: 0.9241 (mttp) cc_final: 0.9015 (mmtp) REVERT: D 133 TYR cc_start: 0.8700 (t80) cc_final: 0.8493 (t80) REVERT: D 135 HIS cc_start: 0.7245 (p-80) cc_final: 0.6999 (p-80) REVERT: D 179 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7305 (mt-10) REVERT: D 183 GLN cc_start: 0.7192 (pm20) cc_final: 0.6519 (pm20) REVERT: D 203 GLN cc_start: 0.8803 (tp40) cc_final: 0.8139 (tp40) REVERT: D 204 ASP cc_start: 0.8844 (m-30) cc_final: 0.8540 (m-30) REVERT: D 213 ASP cc_start: 0.8652 (t0) cc_final: 0.8284 (t0) REVERT: D 228 GLN cc_start: 0.8265 (tt0) cc_final: 0.7640 (tm-30) REVERT: D 230 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7542 (mt-10) REVERT: D 238 LEU cc_start: 0.8979 (mt) cc_final: 0.8729 (mt) REVERT: D 242 GLN cc_start: 0.8165 (tp40) cc_final: 0.7808 (tp-100) REVERT: D 260 ASP cc_start: 0.8084 (t0) cc_final: 0.7844 (t0) REVERT: D 261 LEU cc_start: 0.8498 (pt) cc_final: 0.8119 (pt) REVERT: A 46 THR cc_start: 0.8310 (t) cc_final: 0.8005 (t) REVERT: A 54 HIS cc_start: 0.7586 (m-70) cc_final: 0.7045 (m-70) REVERT: A 79 ASN cc_start: 0.7728 (t0) cc_final: 0.7461 (t0) REVERT: A 90 THR cc_start: 0.8581 (p) cc_final: 0.8358 (t) REVERT: A 108 PHE cc_start: 0.8840 (p90) cc_final: 0.8580 (p90) REVERT: A 133 TYR cc_start: 0.8759 (t80) cc_final: 0.8414 (t80) REVERT: A 176 GLN cc_start: 0.7175 (tm-30) cc_final: 0.6764 (tm-30) REVERT: A 197 ARG cc_start: 0.6449 (ttt180) cc_final: 0.6087 (ttt180) REVERT: A 203 GLN cc_start: 0.8833 (tp40) cc_final: 0.8309 (tp40) REVERT: A 204 ASP cc_start: 0.8890 (m-30) cc_final: 0.8670 (m-30) REVERT: A 227 ARG cc_start: 0.8796 (mtt180) cc_final: 0.8385 (mtt180) REVERT: A 230 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7592 (mt-10) REVERT: A 236 ASN cc_start: 0.8794 (p0) cc_final: 0.8330 (t0) REVERT: A 260 ASP cc_start: 0.8050 (t0) cc_final: 0.7748 (t0) REVERT: A 261 LEU cc_start: 0.8234 (pt) cc_final: 0.7892 (pt) REVERT: A 269 ASN cc_start: 0.8154 (m-40) cc_final: 0.7336 (m-40) REVERT: E 46 THR cc_start: 0.8336 (t) cc_final: 0.7785 (p) REVERT: E 63 GLN cc_start: 0.8920 (mt0) cc_final: 0.8426 (mp10) REVERT: E 79 ASN cc_start: 0.8023 (t0) cc_final: 0.7618 (t0) REVERT: E 108 PHE cc_start: 0.9001 (p90) cc_final: 0.8420 (p90) REVERT: E 129 LYS cc_start: 0.9098 (mttp) cc_final: 0.8797 (mmtp) REVERT: E 133 TYR cc_start: 0.8791 (t80) cc_final: 0.8392 (t80) REVERT: E 135 HIS cc_start: 0.7946 (p-80) cc_final: 0.7549 (p-80) REVERT: E 182 HIS cc_start: 0.7531 (m170) cc_final: 0.7248 (m170) REVERT: E 203 GLN cc_start: 0.8912 (tp40) cc_final: 0.8235 (tp40) REVERT: E 204 ASP cc_start: 0.8796 (m-30) cc_final: 0.8452 (m-30) REVERT: E 227 ARG cc_start: 0.8736 (mtt180) cc_final: 0.8510 (mtt180) REVERT: E 230 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7533 (mt-10) REVERT: E 269 ASN cc_start: 0.7828 (m-40) cc_final: 0.7239 (m-40) REVERT: F 62 GLN cc_start: 0.8871 (mm110) cc_final: 0.8370 (mm110) REVERT: F 79 ASN cc_start: 0.7868 (t0) cc_final: 0.7545 (t0) REVERT: F 108 PHE cc_start: 0.9001 (p90) cc_final: 0.8652 (p90) REVERT: F 129 LYS cc_start: 0.9191 (mttp) cc_final: 0.8962 (tppt) REVERT: F 130 ASP cc_start: 0.8012 (t0) cc_final: 0.7803 (t0) REVERT: F 176 GLN cc_start: 0.6997 (tm-30) cc_final: 0.6601 (tm-30) REVERT: F 203 GLN cc_start: 0.8821 (tp40) cc_final: 0.7983 (tp40) REVERT: F 204 ASP cc_start: 0.8897 (m-30) cc_final: 0.8465 (m-30) REVERT: F 226 ILE cc_start: 0.9055 (tp) cc_final: 0.8801 (tp) REVERT: F 227 ARG cc_start: 0.8814 (mtt180) cc_final: 0.8225 (mtt180) REVERT: F 228 GLN cc_start: 0.8542 (tt0) cc_final: 0.7950 (tm-30) REVERT: F 230 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7611 (mt-10) REVERT: F 243 LYS cc_start: 0.8805 (tmtt) cc_final: 0.8514 (tptp) REVERT: F 263 TRP cc_start: 0.8472 (m100) cc_final: 0.8006 (m100) REVERT: F 269 ASN cc_start: 0.8194 (m-40) cc_final: 0.7311 (m-40) REVERT: F 277 TRP cc_start: 0.7986 (t-100) cc_final: 0.7414 (t-100) REVERT: G 37 ILE cc_start: 0.8406 (pt) cc_final: 0.7823 (mt) REVERT: G 79 ASN cc_start: 0.8236 (t0) cc_final: 0.7906 (t0) REVERT: G 108 PHE cc_start: 0.9172 (p90) cc_final: 0.8765 (p90) REVERT: G 116 THR cc_start: 0.8855 (t) cc_final: 0.8492 (t) REVERT: G 117 GLN cc_start: 0.8306 (mm110) cc_final: 0.8064 (mm110) REVERT: G 149 PRO cc_start: 0.8923 (Cg_exo) cc_final: 0.8571 (Cg_endo) REVERT: G 179 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7404 (mt-10) REVERT: G 182 HIS cc_start: 0.8167 (m-70) cc_final: 0.7184 (m170) REVERT: G 203 GLN cc_start: 0.8931 (tp40) cc_final: 0.7725 (tp40) REVERT: G 204 ASP cc_start: 0.8851 (m-30) cc_final: 0.8505 (m-30) REVERT: G 227 ARG cc_start: 0.8842 (mtt180) cc_final: 0.8192 (mtt180) REVERT: G 230 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7709 (mt-10) REVERT: G 241 ILE cc_start: 0.8943 (pt) cc_final: 0.8588 (pt) REVERT: G 263 TRP cc_start: 0.8297 (m100) cc_final: 0.7839 (m100) REVERT: G 269 ASN cc_start: 0.7579 (m-40) cc_final: 0.7112 (m-40) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.1317 time to fit residues: 87.7864 Evaluate side-chains 423 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 85 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 29 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 0.0570 chunk 115 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN B 146 HIS B 228 GLN C 228 GLN D 117 GLN ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS D 228 GLN A 117 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN F 228 GLN F 273 GLN G 146 HIS G 228 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.085099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.070434 restraints weight = 46521.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.073308 restraints weight = 26706.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.075316 restraints weight = 17674.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.076755 restraints weight = 12849.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.077666 restraints weight = 9982.484| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.441 16952 Z= 0.193 Angle : 0.887 12.093 23765 Z= 0.342 Chirality : 0.048 0.150 2128 Planarity : 0.005 0.046 2912 Dihedral : 18.080 89.813 2303 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.20), residues: 1792 helix: -2.01 (0.27), residues: 287 sheet: -2.15 (0.58), residues: 70 loop : -1.49 (0.18), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 197 TYR 0.012 0.002 TYR B 151 PHE 0.013 0.002 PHE F 42 TRP 0.023 0.001 TRP F 279 HIS 0.010 0.001 HIS G 276 Details of bonding type rmsd covalent geometry : bond 0.00538 (16772) covalent geometry : angle 0.88654 (23765) hydrogen bonds : bond 0.03274 ( 154) hydrogen bonds : angle 6.75200 ( 441) Misc. bond : bond 0.14013 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 450 time to evaluate : 0.447 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: 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: B 63 GLN cc_start: 0.8851 (mt0) cc_final: 0.8349 (mp10) REVERT: B 79 ASN cc_start: 0.8106 (t0) cc_final: 0.7850 (t0) REVERT: B 95 MET cc_start: 0.8709 (mmm) cc_final: 0.8355 (mmp) REVERT: B 108 PHE cc_start: 0.8971 (p90) cc_final: 0.8675 (p90) REVERT: B 149 PRO cc_start: 0.9158 (Cg_exo) cc_final: 0.8912 (Cg_endo) REVERT: B 151 TYR cc_start: 0.8774 (p90) cc_final: 0.8522 (p90) REVERT: B 176 GLN cc_start: 0.7552 (tm-30) cc_final: 0.7219 (tm-30) REVERT: B 200 PHE cc_start: 0.8114 (m-10) cc_final: 0.7232 (m-10) REVERT: B 203 GLN cc_start: 0.8770 (tp40) cc_final: 0.8273 (tp40) REVERT: B 204 ASP cc_start: 0.8829 (m-30) cc_final: 0.7712 (t0) REVERT: B 227 ARG cc_start: 0.9138 (mtt180) cc_final: 0.8572 (mtt180) REVERT: B 230 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7593 (mt-10) REVERT: B 238 LEU cc_start: 0.9117 (mp) cc_final: 0.8913 (mp) REVERT: B 243 LYS cc_start: 0.9023 (tptp) cc_final: 0.8756 (tptp) REVERT: B 255 LYS cc_start: 0.8833 (ptpp) cc_final: 0.8555 (pttm) REVERT: C 90 THR cc_start: 0.8503 (p) cc_final: 0.8256 (t) REVERT: C 95 MET cc_start: 0.8604 (mmp) cc_final: 0.8329 (mmp) REVERT: C 108 PHE cc_start: 0.9067 (p90) cc_final: 0.8372 (p90) REVERT: C 109 ARG cc_start: 0.9071 (mmt180) cc_final: 0.8704 (mmt180) REVERT: C 129 LYS cc_start: 0.9141 (mmtm) cc_final: 0.8748 (tppp) REVERT: C 135 HIS cc_start: 0.7319 (p90) cc_final: 0.6939 (p90) REVERT: C 149 PRO cc_start: 0.8803 (Cg_exo) cc_final: 0.8494 (Cg_endo) REVERT: C 179 GLU cc_start: 0.7510 (tt0) cc_final: 0.6733 (tm-30) REVERT: C 182 HIS cc_start: 0.8355 (m-70) cc_final: 0.8005 (m170) REVERT: C 183 GLN cc_start: 0.5795 (pm20) cc_final: 0.5392 (pm20) REVERT: C 203 GLN cc_start: 0.8767 (tp40) cc_final: 0.7723 (tp40) REVERT: C 204 ASP cc_start: 0.8799 (m-30) cc_final: 0.8464 (m-30) REVERT: C 227 ARG cc_start: 0.8720 (mtt180) cc_final: 0.8298 (mtt180) REVERT: C 228 GLN cc_start: 0.8502 (tt0) cc_final: 0.8052 (tm-30) REVERT: C 230 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7581 (mt-10) REVERT: C 238 LEU cc_start: 0.8935 (mt) cc_final: 0.8550 (mp) REVERT: C 243 LYS cc_start: 0.8944 (tptp) cc_final: 0.8510 (tptp) REVERT: C 255 LYS cc_start: 0.8716 (ptpp) cc_final: 0.8441 (ptpp) REVERT: C 263 TRP cc_start: 0.8300 (m100) cc_final: 0.7846 (m100) REVERT: C 269 ASN cc_start: 0.7462 (m-40) cc_final: 0.6912 (m-40) REVERT: D 46 THR cc_start: 0.7982 (t) cc_final: 0.7715 (t) REVERT: D 51 LEU cc_start: 0.7609 (mt) cc_final: 0.7364 (mt) REVERT: D 62 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8311 (mm110) REVERT: D 79 ASN cc_start: 0.7936 (t0) cc_final: 0.7635 (t0) REVERT: D 108 PHE cc_start: 0.8974 (p90) cc_final: 0.8080 (p90) REVERT: D 109 ARG cc_start: 0.9156 (mmt180) cc_final: 0.8915 (mmt180) REVERT: D 129 LYS cc_start: 0.9212 (mttp) cc_final: 0.8984 (mmtp) REVERT: D 179 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7256 (mt-10) REVERT: D 183 GLN cc_start: 0.7180 (pm20) cc_final: 0.6474 (pm20) REVERT: D 200 PHE cc_start: 0.8143 (m-10) cc_final: 0.7551 (m-10) REVERT: D 203 GLN cc_start: 0.8761 (tp40) cc_final: 0.8090 (tp40) REVERT: D 204 ASP cc_start: 0.8829 (m-30) cc_final: 0.7928 (t0) REVERT: D 213 ASP cc_start: 0.8651 (t0) cc_final: 0.8272 (t0) REVERT: D 230 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7575 (mt-10) REVERT: D 238 LEU cc_start: 0.8984 (mt) cc_final: 0.8742 (mt) REVERT: D 242 GLN cc_start: 0.8203 (tp40) cc_final: 0.7795 (tp-100) REVERT: D 260 ASP cc_start: 0.8052 (t0) cc_final: 0.7830 (t0) REVERT: D 261 LEU cc_start: 0.8389 (pt) cc_final: 0.8035 (pt) REVERT: D 269 ASN cc_start: 0.7689 (m-40) cc_final: 0.7119 (m-40) REVERT: D 271 ASP cc_start: 0.8069 (p0) cc_final: 0.7700 (p0) REVERT: A 54 HIS cc_start: 0.7619 (m-70) cc_final: 0.7093 (m-70) REVERT: A 63 GLN cc_start: 0.8633 (pt0) cc_final: 0.8355 (mp10) REVERT: A 79 ASN cc_start: 0.7661 (t0) cc_final: 0.7422 (t0) REVERT: A 90 THR cc_start: 0.8603 (p) cc_final: 0.8371 (t) REVERT: A 108 PHE cc_start: 0.8916 (p90) cc_final: 0.8683 (p90) REVERT: A 133 TYR cc_start: 0.8716 (t80) cc_final: 0.8384 (t80) REVERT: A 169 ASP cc_start: 0.7042 (t0) cc_final: 0.6707 (p0) REVERT: A 176 GLN cc_start: 0.7334 (tm-30) cc_final: 0.6809 (tm-30) REVERT: A 203 GLN cc_start: 0.8815 (tp40) cc_final: 0.8269 (tp40) REVERT: A 204 ASP cc_start: 0.8884 (m-30) cc_final: 0.8585 (m-30) REVERT: A 226 ILE cc_start: 0.9010 (tp) cc_final: 0.8807 (tp) REVERT: A 227 ARG cc_start: 0.8691 (mtt180) cc_final: 0.8307 (mtt180) REVERT: A 228 GLN cc_start: 0.8491 (tt0) cc_final: 0.7973 (tm-30) REVERT: A 230 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7331 (mt-10) REVERT: A 236 ASN cc_start: 0.8706 (p0) cc_final: 0.8365 (t0) REVERT: A 260 ASP cc_start: 0.8011 (t0) cc_final: 0.7713 (t0) REVERT: A 261 LEU cc_start: 0.8234 (pt) cc_final: 0.7851 (pt) REVERT: A 269 ASN cc_start: 0.7677 (m-40) cc_final: 0.6992 (m-40) REVERT: E 46 THR cc_start: 0.8282 (t) cc_final: 0.7730 (p) REVERT: E 63 GLN cc_start: 0.8916 (mt0) cc_final: 0.8457 (mt0) REVERT: E 79 ASN cc_start: 0.7984 (t0) cc_final: 0.7640 (t0) REVERT: E 108 PHE cc_start: 0.9006 (p90) cc_final: 0.8608 (p90) REVERT: E 129 LYS cc_start: 0.9102 (mttp) cc_final: 0.8804 (mmtp) REVERT: E 133 TYR cc_start: 0.8737 (t80) cc_final: 0.8347 (t80) REVERT: E 135 HIS cc_start: 0.7898 (p-80) cc_final: 0.7497 (p-80) REVERT: E 182 HIS cc_start: 0.7566 (m170) cc_final: 0.7049 (m-70) REVERT: E 183 GLN cc_start: 0.7562 (pm20) cc_final: 0.7358 (pm20) REVERT: E 203 GLN cc_start: 0.8897 (tp40) cc_final: 0.8232 (tp40) REVERT: E 204 ASP cc_start: 0.8781 (m-30) cc_final: 0.8449 (m-30) REVERT: E 227 ARG cc_start: 0.8700 (mtt180) cc_final: 0.8333 (mtt180) REVERT: E 230 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7592 (mt-10) REVERT: E 261 LEU cc_start: 0.8116 (pt) cc_final: 0.7876 (pp) REVERT: E 269 ASN cc_start: 0.7750 (m-40) cc_final: 0.7023 (m-40) REVERT: F 61 VAL cc_start: 0.9239 (m) cc_final: 0.8882 (p) REVERT: F 62 GLN cc_start: 0.8929 (mm110) cc_final: 0.8376 (mm110) REVERT: F 79 ASN cc_start: 0.7823 (t0) cc_final: 0.7520 (t0) REVERT: F 108 PHE cc_start: 0.9039 (p90) cc_final: 0.8630 (p90) REVERT: F 129 LYS cc_start: 0.9158 (mttp) cc_final: 0.8936 (tppt) REVERT: F 130 ASP cc_start: 0.7985 (t0) cc_final: 0.7770 (t0) REVERT: F 179 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7274 (mt-10) REVERT: F 203 GLN cc_start: 0.8814 (tp40) cc_final: 0.7930 (tp40) REVERT: F 204 ASP cc_start: 0.8875 (m-30) cc_final: 0.8433 (m-30) REVERT: F 226 ILE cc_start: 0.9031 (tp) cc_final: 0.8803 (tp) REVERT: F 227 ARG cc_start: 0.8867 (mtt180) cc_final: 0.8385 (mtt180) REVERT: F 230 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7645 (mt-10) REVERT: F 243 LYS cc_start: 0.8796 (tmtt) cc_final: 0.8522 (tptp) REVERT: F 263 TRP cc_start: 0.8427 (m100) cc_final: 0.7967 (m100) REVERT: F 269 ASN cc_start: 0.7669 (m-40) cc_final: 0.6998 (m-40) REVERT: F 277 TRP cc_start: 0.8009 (t-100) cc_final: 0.7453 (t-100) REVERT: G 46 THR cc_start: 0.8179 (t) cc_final: 0.7978 (t) REVERT: G 54 HIS cc_start: 0.7464 (m-70) cc_final: 0.7123 (m-70) REVERT: G 79 ASN cc_start: 0.8302 (t0) cc_final: 0.7959 (t0) REVERT: G 107 ASP cc_start: 0.8339 (t0) cc_final: 0.7844 (t0) REVERT: G 108 PHE cc_start: 0.9170 (p90) cc_final: 0.8789 (p90) REVERT: G 135 HIS cc_start: 0.6979 (p90) cc_final: 0.6622 (p90) REVERT: G 149 PRO cc_start: 0.8890 (Cg_exo) cc_final: 0.8473 (Cg_endo) REVERT: G 179 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7323 (mt-10) REVERT: G 182 HIS cc_start: 0.8071 (m-70) cc_final: 0.7099 (m170) REVERT: G 203 GLN cc_start: 0.8901 (tp40) cc_final: 0.7737 (tp40) REVERT: G 204 ASP cc_start: 0.8831 (m-30) cc_final: 0.8585 (m-30) REVERT: G 226 ILE cc_start: 0.8904 (tp) cc_final: 0.8687 (tp) REVERT: G 227 ARG cc_start: 0.8720 (mtt180) cc_final: 0.7989 (mtt180) REVERT: G 228 GLN cc_start: 0.8473 (tt0) cc_final: 0.7800 (tm-30) REVERT: G 230 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7631 (mt-10) REVERT: G 241 ILE cc_start: 0.8953 (pt) cc_final: 0.8658 (pt) outliers start: 0 outliers final: 0 residues processed: 450 average time/residue: 0.1285 time to fit residues: 84.7172 Evaluate side-chains 422 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 156 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 157 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 0.0060 chunk 103 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS B 228 GLN C 228 GLN D 117 GLN ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN A 146 HIS A 228 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 GLN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 GLN G 146 HIS G 228 GLN ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.084972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.069903 restraints weight = 46579.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.072895 restraints weight = 26124.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.075003 restraints weight = 17099.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.076520 restraints weight = 12272.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.077592 restraints weight = 9456.444| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.463 16952 Z= 0.202 Angle : 0.898 11.880 23765 Z= 0.345 Chirality : 0.048 0.142 2128 Planarity : 0.005 0.045 2912 Dihedral : 18.072 89.813 2303 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.67 % Favored : 86.33 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.20), residues: 1792 helix: -2.03 (0.26), residues: 294 sheet: -2.30 (0.58), residues: 70 loop : -1.55 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 197 TYR 0.013 0.002 TYR B 151 PHE 0.014 0.002 PHE A 42 TRP 0.022 0.001 TRP F 279 HIS 0.009 0.001 HIS G 276 Details of bonding type rmsd covalent geometry : bond 0.00565 (16772) covalent geometry : angle 0.89765 (23765) hydrogen bonds : bond 0.03290 ( 154) hydrogen bonds : angle 6.78628 ( 441) Misc. bond : bond 0.14723 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 0.540 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: 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: B 63 GLN cc_start: 0.8869 (mt0) cc_final: 0.8358 (mp10) REVERT: B 79 ASN cc_start: 0.8108 (t0) cc_final: 0.7864 (t0) REVERT: B 95 MET cc_start: 0.8701 (mmm) cc_final: 0.8464 (mmp) REVERT: B 108 PHE cc_start: 0.9018 (p90) cc_final: 0.8781 (p90) REVERT: B 109 ARG cc_start: 0.8944 (mmm-85) cc_final: 0.8711 (mmm160) REVERT: B 149 PRO cc_start: 0.9159 (Cg_exo) cc_final: 0.8905 (Cg_endo) REVERT: B 151 TYR cc_start: 0.8822 (p90) cc_final: 0.8579 (p90) REVERT: B 176 GLN cc_start: 0.7370 (tm-30) cc_final: 0.6909 (tm-30) REVERT: B 203 GLN cc_start: 0.8771 (tp40) cc_final: 0.8326 (tp40) REVERT: B 204 ASP cc_start: 0.8785 (m-30) cc_final: 0.7881 (t0) REVERT: B 227 ARG cc_start: 0.9061 (mtt180) cc_final: 0.8398 (mtt180) REVERT: B 228 GLN cc_start: 0.8443 (tt0) cc_final: 0.7999 (tm-30) REVERT: B 230 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7550 (mt-10) REVERT: B 238 LEU cc_start: 0.9110 (mp) cc_final: 0.8907 (mp) REVERT: B 243 LYS cc_start: 0.9036 (tptp) cc_final: 0.8770 (tptp) REVERT: B 255 LYS cc_start: 0.8843 (ptpp) cc_final: 0.8603 (ptpp) REVERT: C 63 GLN cc_start: 0.8534 (pt0) cc_final: 0.8313 (mp10) REVERT: C 90 THR cc_start: 0.8594 (p) cc_final: 0.8361 (t) REVERT: C 95 MET cc_start: 0.8592 (mmp) cc_final: 0.8263 (mmp) REVERT: C 108 PHE cc_start: 0.9046 (p90) cc_final: 0.8367 (p90) REVERT: C 109 ARG cc_start: 0.9060 (mmt180) cc_final: 0.8652 (mmt180) REVERT: C 129 LYS cc_start: 0.9187 (mmtm) cc_final: 0.8766 (tppp) REVERT: C 135 HIS cc_start: 0.7334 (p90) cc_final: 0.6962 (p90) REVERT: C 139 ILE cc_start: 0.8733 (tp) cc_final: 0.8521 (tp) REVERT: C 149 PRO cc_start: 0.8861 (Cg_exo) cc_final: 0.8627 (Cg_endo) REVERT: C 179 GLU cc_start: 0.7366 (tt0) cc_final: 0.6660 (tm-30) REVERT: C 182 HIS cc_start: 0.8314 (m-70) cc_final: 0.7928 (m170) REVERT: C 183 GLN cc_start: 0.5565 (pm20) cc_final: 0.5158 (pm20) REVERT: C 200 PHE cc_start: 0.7992 (m-80) cc_final: 0.7156 (m-10) REVERT: C 203 GLN cc_start: 0.8763 (tp40) cc_final: 0.7678 (tp40) REVERT: C 204 ASP cc_start: 0.8846 (m-30) cc_final: 0.7688 (t0) REVERT: C 227 ARG cc_start: 0.8733 (mtt180) cc_final: 0.8363 (mtt180) REVERT: C 230 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7600 (mt-10) REVERT: C 238 LEU cc_start: 0.8919 (mt) cc_final: 0.8533 (mp) REVERT: C 243 LYS cc_start: 0.8960 (tptp) cc_final: 0.8518 (tptp) REVERT: C 255 LYS cc_start: 0.8724 (ptpp) cc_final: 0.8444 (ptpp) REVERT: C 263 TRP cc_start: 0.8295 (m100) cc_final: 0.7859 (m100) REVERT: C 269 ASN cc_start: 0.7472 (m-40) cc_final: 0.6928 (m-40) REVERT: D 46 THR cc_start: 0.8106 (t) cc_final: 0.7844 (t) REVERT: D 51 LEU cc_start: 0.7626 (mt) cc_final: 0.7385 (mt) REVERT: D 62 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8412 (mm110) REVERT: D 79 ASN cc_start: 0.7925 (t0) cc_final: 0.7646 (t0) REVERT: D 108 PHE cc_start: 0.8980 (p90) cc_final: 0.8090 (p90) REVERT: D 109 ARG cc_start: 0.9142 (mmt180) cc_final: 0.8883 (mmt180) REVERT: D 129 LYS cc_start: 0.9173 (mttp) cc_final: 0.8945 (mmtp) REVERT: D 179 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7255 (mt-10) REVERT: D 183 GLN cc_start: 0.7165 (pm20) cc_final: 0.6542 (pm20) REVERT: D 203 GLN cc_start: 0.8777 (tp40) cc_final: 0.8109 (tp40) REVERT: D 204 ASP cc_start: 0.8825 (m-30) cc_final: 0.8506 (m-30) REVERT: D 213 ASP cc_start: 0.8652 (t0) cc_final: 0.8262 (t0) REVERT: D 228 GLN cc_start: 0.8220 (tt0) cc_final: 0.7593 (tm-30) REVERT: D 230 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7538 (mt-10) REVERT: D 238 LEU cc_start: 0.8945 (mt) cc_final: 0.8656 (mt) REVERT: D 242 GLN cc_start: 0.8210 (tp40) cc_final: 0.7795 (tp-100) REVERT: D 260 ASP cc_start: 0.8052 (t0) cc_final: 0.7837 (t0) REVERT: D 261 LEU cc_start: 0.8378 (pt) cc_final: 0.8024 (pt) REVERT: D 269 ASN cc_start: 0.7797 (m-40) cc_final: 0.7386 (m-40) REVERT: D 271 ASP cc_start: 0.8000 (p0) cc_final: 0.7736 (p0) REVERT: A 37 ILE cc_start: 0.8441 (pt) cc_final: 0.7962 (mt) REVERT: A 54 HIS cc_start: 0.7590 (m-70) cc_final: 0.6998 (m-70) REVERT: A 79 ASN cc_start: 0.7695 (t0) cc_final: 0.7461 (t0) REVERT: A 90 THR cc_start: 0.8624 (p) cc_final: 0.8405 (t) REVERT: A 95 MET cc_start: 0.9012 (mmp) cc_final: 0.8696 (mmm) REVERT: A 109 ARG cc_start: 0.8868 (mmt180) cc_final: 0.8588 (tpp-160) REVERT: A 129 LYS cc_start: 0.9299 (mmtp) cc_final: 0.8970 (tppt) REVERT: A 133 TYR cc_start: 0.8695 (t80) cc_final: 0.8363 (t80) REVERT: A 169 ASP cc_start: 0.6966 (t0) cc_final: 0.6612 (p0) REVERT: A 176 GLN cc_start: 0.7330 (tm-30) cc_final: 0.6818 (tm-30) REVERT: A 197 ARG cc_start: 0.6888 (ttt180) cc_final: 0.6674 (ttt180) REVERT: A 203 GLN cc_start: 0.8833 (tp40) cc_final: 0.8268 (tp40) REVERT: A 204 ASP cc_start: 0.8896 (m-30) cc_final: 0.8583 (m-30) REVERT: A 227 ARG cc_start: 0.8738 (mtt180) cc_final: 0.8316 (mtt180) REVERT: A 230 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7338 (mt-10) REVERT: A 236 ASN cc_start: 0.8744 (p0) cc_final: 0.8442 (t0) REVERT: A 260 ASP cc_start: 0.8001 (t0) cc_final: 0.7720 (t0) REVERT: A 261 LEU cc_start: 0.8197 (pt) cc_final: 0.7844 (pt) REVERT: A 269 ASN cc_start: 0.8105 (m-40) cc_final: 0.7316 (m-40) REVERT: E 46 THR cc_start: 0.8298 (t) cc_final: 0.7774 (p) REVERT: E 63 GLN cc_start: 0.8925 (mt0) cc_final: 0.8456 (mt0) REVERT: E 79 ASN cc_start: 0.7964 (t0) cc_final: 0.7583 (t0) REVERT: E 108 PHE cc_start: 0.8907 (p90) cc_final: 0.8645 (p90) REVERT: E 129 LYS cc_start: 0.9107 (mttp) cc_final: 0.8808 (mmtp) REVERT: E 133 TYR cc_start: 0.8728 (t80) cc_final: 0.8344 (t80) REVERT: E 135 HIS cc_start: 0.7928 (p-80) cc_final: 0.7534 (p-80) REVERT: E 182 HIS cc_start: 0.7568 (m170) cc_final: 0.7021 (m-70) REVERT: E 203 GLN cc_start: 0.8889 (tp40) cc_final: 0.8282 (tp40) REVERT: E 227 ARG cc_start: 0.8679 (mtt180) cc_final: 0.8253 (mtt180) REVERT: E 230 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7570 (mt-10) REVERT: E 261 LEU cc_start: 0.8055 (pt) cc_final: 0.7846 (pp) REVERT: E 269 ASN cc_start: 0.8120 (m-40) cc_final: 0.7156 (m-40) REVERT: F 54 HIS cc_start: 0.7605 (m-70) cc_final: 0.7347 (m-70) REVERT: F 79 ASN cc_start: 0.7815 (t0) cc_final: 0.7553 (t0) REVERT: F 108 PHE cc_start: 0.9010 (p90) cc_final: 0.8661 (p90) REVERT: F 129 LYS cc_start: 0.9157 (mttp) cc_final: 0.8941 (tppt) REVERT: F 130 ASP cc_start: 0.7962 (t0) cc_final: 0.7758 (t0) REVERT: F 176 GLN cc_start: 0.7219 (tm-30) cc_final: 0.6586 (tm-30) REVERT: F 200 PHE cc_start: 0.8128 (m-80) cc_final: 0.7838 (m-10) REVERT: F 203 GLN cc_start: 0.8841 (tp40) cc_final: 0.7911 (tp40) REVERT: F 204 ASP cc_start: 0.8869 (m-30) cc_final: 0.7886 (t0) REVERT: F 226 ILE cc_start: 0.9038 (tp) cc_final: 0.8685 (tp) REVERT: F 228 GLN cc_start: 0.8522 (tt0) cc_final: 0.7994 (tm-30) REVERT: F 229 CYS cc_start: 0.7627 (m) cc_final: 0.7330 (p) REVERT: F 230 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7569 (mt-10) REVERT: F 243 LYS cc_start: 0.8805 (tmtt) cc_final: 0.8531 (tptp) REVERT: F 263 TRP cc_start: 0.8425 (m100) cc_final: 0.7930 (m100) REVERT: F 269 ASN cc_start: 0.8188 (m-40) cc_final: 0.7282 (m-40) REVERT: F 277 TRP cc_start: 0.7955 (t-100) cc_final: 0.7428 (t-100) REVERT: G 54 HIS cc_start: 0.7411 (m-70) cc_final: 0.7037 (m-70) REVERT: G 107 ASP cc_start: 0.8522 (t0) cc_final: 0.7909 (t0) REVERT: G 108 PHE cc_start: 0.9187 (p90) cc_final: 0.8829 (p90) REVERT: G 129 LYS cc_start: 0.9318 (mttm) cc_final: 0.9062 (tppt) REVERT: G 135 HIS cc_start: 0.6998 (p90) cc_final: 0.6620 (p90) REVERT: G 149 PRO cc_start: 0.8998 (Cg_exo) cc_final: 0.8613 (Cg_endo) REVERT: G 179 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7296 (mt-10) REVERT: G 182 HIS cc_start: 0.8102 (m-70) cc_final: 0.7159 (m-70) REVERT: G 203 GLN cc_start: 0.8899 (tp40) cc_final: 0.7702 (tp40) REVERT: G 204 ASP cc_start: 0.8831 (m-30) cc_final: 0.7907 (t0) REVERT: G 227 ARG cc_start: 0.8733 (mtt180) cc_final: 0.8111 (mtt180) REVERT: G 230 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7701 (mt-10) REVERT: G 241 ILE cc_start: 0.8942 (pt) cc_final: 0.8650 (pt) REVERT: G 243 LYS cc_start: 0.8708 (tmtt) cc_final: 0.8337 (tptp) REVERT: G 263 TRP cc_start: 0.8257 (m100) cc_final: 0.7936 (m100) REVERT: G 269 ASN cc_start: 0.7823 (m-40) cc_final: 0.7300 (m-40) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.1301 time to fit residues: 86.4234 Evaluate side-chains 422 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 57 optimal weight: 0.7980 chunk 169 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 28 optimal weight: 0.0670 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 97 optimal weight: 0.3980 chunk 79 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS B 228 GLN C 63 GLN C 228 GLN ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS D 228 GLN D 273 GLN A 117 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 GLN F 273 GLN G 117 GLN G 146 HIS G 228 GLN ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.085711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.070585 restraints weight = 46038.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.073595 restraints weight = 26007.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.075689 restraints weight = 17085.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.077166 restraints weight = 12328.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.078242 restraints weight = 9577.332| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.432 16952 Z= 0.183 Angle : 0.877 11.409 23765 Z= 0.336 Chirality : 0.048 0.149 2128 Planarity : 0.005 0.041 2912 Dihedral : 18.041 89.438 2303 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.23 % Favored : 86.77 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.20), residues: 1792 helix: -1.98 (0.26), residues: 294 sheet: -2.36 (0.58), residues: 70 loop : -1.55 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 197 TYR 0.012 0.002 TYR B 151 PHE 0.014 0.002 PHE D 103 TRP 0.022 0.001 TRP F 279 HIS 0.008 0.001 HIS G 276 Details of bonding type rmsd covalent geometry : bond 0.00509 (16772) covalent geometry : angle 0.87706 (23765) hydrogen bonds : bond 0.03110 ( 154) hydrogen bonds : angle 6.58322 ( 441) Misc. bond : bond 0.13406 ( 180) =============================================================================== Job complete usr+sys time: 2862.29 seconds wall clock time: 50 minutes 9.59 seconds (3009.59 seconds total)