Starting phenix.real_space_refine on Sat Jun 14 06:42:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d9m_27266/06_2025/8d9m_27266.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d9m_27266/06_2025/8d9m_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d9m_27266/06_2025/8d9m_27266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d9m_27266/06_2025/8d9m_27266.map" model { file = "/net/cci-nas-00/data/ceres_data/8d9m_27266/06_2025/8d9m_27266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d9m_27266/06_2025/8d9m_27266.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15967 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" 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: "A" 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, B, E, D, G, F Time building chain proxies: 6.07, per 1000 atoms: 0.38 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: 4.94 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.43 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: 3.13 Time building geometry restraints manager: 5.77 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 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: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 32.330 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.030 ------------------------------------------------------------------------------- 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 : 31.60 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (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 TRP 0.016 0.002 TRP G 270 HIS 0.015 0.002 HIS D 135 PHE 0.021 0.003 PHE G 42 TYR 0.012 0.003 TYR E 147 ARG 0.003 0.000 ARG F 227 Details of bonding type rmsd hydrogen bonds : bond 0.17048 ( 154) hydrogen bonds : angle 8.92912 ( 441) covalent geometry : bond 0.00738 (16772) covalent geometry : angle 1.02295 (23765) 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 : 1.508 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: B 61 VAL cc_start: 0.9141 (m) cc_final: 0.8908 (p) REVERT: B 79 ASN cc_start: 0.7926 (t0) cc_final: 0.7480 (t0) REVERT: B 95 MET cc_start: 0.8635 (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: 0.8261 (t-100) cc_final: 0.7740 (t-100) REVERT: C 51 LEU cc_start: 0.7716 (mt) cc_final: 0.7515 (mt) REVERT: C 79 ASN cc_start: 0.7750 (t0) cc_final: 0.7429 (t0) REVERT: C 95 MET cc_start: 0.8712 (mmm) cc_final: 0.8129 (mmp) REVERT: C 116 THR cc_start: 0.8837 (m) cc_final: 0.8339 (t) REVERT: C 148 ILE cc_start: 0.9148 (mm) cc_final: 0.8879 (mm) REVERT: C 179 GLU cc_start: 0.7991 (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: 0.7420 (mt) REVERT: D 79 ASN cc_start: 0.7874 (t0) cc_final: 0.7501 (t0) REVERT: D 108 PHE cc_start: 0.8734 (p90) cc_final: 0.8468 (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: 0.7591 (mt-10) REVERT: D 203 GLN cc_start: 0.8905 (tp40) cc_final: 0.8300 (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: 0.7938 (m-40) REVERT: A 37 ILE cc_start: 0.8675 (pt) cc_final: 0.8428 (pt) REVERT: A 61 VAL cc_start: 0.9208 (m) cc_final: 0.9005 (p) REVERT: A 176 GLN cc_start: 0.7590 (tm-30) cc_final: 0.7110 (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: 0.8730 (tp) REVERT: A 227 ARG cc_start: 0.9004 (mtt180) cc_final: 0.8411 (mmt180) REVERT: A 230 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7470 (mt-10) REVERT: A 269 ASN cc_start: 0.8214 (m-40) cc_final: 0.7702 (m-40) REVERT: E 61 VAL cc_start: 0.9144 (m) cc_final: 0.8926 (p) REVERT: E 79 ASN cc_start: 0.7914 (t0) cc_final: 0.7386 (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: 0.8986 (mm) REVERT: E 179 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7364 (mt-10) REVERT: E 203 GLN cc_start: 0.8933 (tp40) cc_final: 0.8544 (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: 0.8496 (mt0) REVERT: F 79 ASN cc_start: 0.7905 (t0) cc_final: 0.7596 (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: 0.8554 (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: 0.8046 (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: 0.8601 (t0) REVERT: G 203 GLN cc_start: 0.9043 (tp40) cc_final: 0.8394 (tp40) REVERT: G 204 ASP cc_start: 0.8831 (m-30) cc_final: 0.8593 (m-30) REVERT: G 216 LEU cc_start: 0.8630 (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: 0.2973 time to fit residues: 175.7373 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 : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 chunk 89 optimal weight: 0.0870 chunk 70 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 102 optimal weight: 0.4980 chunk 158 optimal weight: 9.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS E 228 GLN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.086685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.071226 restraints weight = 45192.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.074312 restraints weight = 25625.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.076497 restraints weight = 16852.368| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.409 16952 Z= 0.212 Angle : 0.943 12.934 23765 Z= 0.348 Chirality : 0.048 0.143 2128 Planarity : 0.006 0.071 2912 Dihedral : 17.915 89.004 2303 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.67 % Favored : 87.33 % Rotamer: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.20), residues: 1792 helix: -1.44 (0.28), residues: 287 sheet: -0.48 (0.50), residues: 70 loop : -1.57 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 279 HIS 0.007 0.001 HIS B 64 PHE 0.015 0.002 PHE B 103 TYR 0.013 0.002 TYR E 133 ARG 0.002 0.000 ARG B 227 Details of bonding type rmsd hydrogen bonds : bond 0.03075 ( 154) hydrogen bonds : angle 6.49068 ( 441) covalent geometry : bond 0.00597 (16772) covalent geometry : angle 0.94344 (23765) Misc. bond : bond 0.13971 ( 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 434 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 1.554 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: B 51 LEU cc_start: 0.7707 (mt) cc_final: 0.7503 (mt) REVERT: B 60 LEU cc_start: 0.9146 (mm) cc_final: 0.8889 (pp) REVERT: B 63 GLN cc_start: 0.8810 (mt0) cc_final: 0.8434 (mt0) REVERT: B 79 ASN cc_start: 0.8006 (t0) cc_final: 0.7585 (t0) REVERT: B 95 MET cc_start: 0.8465 (mmm) cc_final: 0.8163 (mmm) REVERT: B 108 PHE cc_start: 0.8881 (p90) cc_final: 0.8674 (p90) REVERT: B 129 LYS cc_start: 0.9339 (ptpp) cc_final: 0.9066 (mttp) REVERT: B 176 GLN cc_start: 0.7423 (tm-30) cc_final: 0.7183 (tm-30) REVERT: B 203 GLN cc_start: 0.9011 (tp40) cc_final: 0.8317 (tp40) REVERT: B 204 ASP cc_start: 0.8957 (m-30) cc_final: 0.8560 (m-30) REVERT: B 243 LYS cc_start: 0.8796 (tmtt) cc_final: 0.8460 (tptp) REVERT: B 263 TRP cc_start: 0.8313 (m100) cc_final: 0.7745 (m100) REVERT: B 269 ASN cc_start: 0.8105 (m-40) cc_final: 0.7377 (t0) REVERT: B 273 GLN cc_start: 0.8545 (mt0) cc_final: 0.8302 (mt0) REVERT: C 51 LEU cc_start: 0.7602 (mt) cc_final: 0.7384 (mt) REVERT: C 79 ASN cc_start: 0.7864 (t0) cc_final: 0.7582 (t0) REVERT: C 90 THR cc_start: 0.8464 (p) cc_final: 0.8200 (t) REVERT: C 95 MET cc_start: 0.8615 (mmm) cc_final: 0.8213 (mmm) REVERT: C 108 PHE cc_start: 0.8924 (p90) cc_final: 0.8459 (p90) REVERT: C 116 THR cc_start: 0.8899 (m) cc_final: 0.8261 (t) REVERT: C 117 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8037 (mm-40) REVERT: C 139 ILE cc_start: 0.8781 (tp) cc_final: 0.8543 (tp) REVERT: C 179 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7551 (mt-10) REVERT: C 182 HIS cc_start: 0.8310 (m-70) cc_final: 0.7638 (m-70) REVERT: C 183 GLN cc_start: 0.4865 (pm20) cc_final: 0.4646 (pm20) REVERT: C 203 GLN cc_start: 0.8950 (tp40) cc_final: 0.8220 (tp40) REVERT: C 204 ASP cc_start: 0.8752 (m-30) cc_final: 0.8549 (m-30) REVERT: C 238 LEU cc_start: 0.8846 (mp) cc_final: 0.8545 (mt) REVERT: C 263 TRP cc_start: 0.8396 (m100) cc_final: 0.7413 (m100) REVERT: C 269 ASN cc_start: 0.7491 (m-40) cc_final: 0.6819 (t0) REVERT: C 279 TRP cc_start: 0.7758 (t-100) cc_final: 0.7365 (t-100) REVERT: D 79 ASN cc_start: 0.7997 (t0) cc_final: 0.7674 (t0) REVERT: D 176 GLN cc_start: 0.7258 (tm-30) cc_final: 0.7005 (tm-30) REVERT: D 203 GLN cc_start: 0.9037 (tp40) cc_final: 0.8378 (tp40) REVERT: D 204 ASP cc_start: 0.8874 (m-30) cc_final: 0.8572 (m-30) REVERT: D 226 ILE cc_start: 0.9027 (tp) cc_final: 0.8818 (tp) REVERT: D 227 ARG cc_start: 0.8826 (mmt180) cc_final: 0.8580 (mtt180) REVERT: D 230 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7721 (mt-10) REVERT: D 242 GLN cc_start: 0.8131 (tp40) cc_final: 0.7839 (tp-100) REVERT: D 269 ASN cc_start: 0.7716 (m-40) cc_final: 0.7157 (t0) REVERT: A 37 ILE cc_start: 0.8635 (pt) cc_final: 0.8285 (pt) REVERT: A 51 LEU cc_start: 0.7655 (mt) cc_final: 0.7444 (mt) REVERT: A 61 VAL cc_start: 0.9318 (m) cc_final: 0.9082 (p) REVERT: A 203 GLN cc_start: 0.8964 (tp40) cc_final: 0.8557 (tp40) REVERT: A 204 ASP cc_start: 0.8826 (m-30) cc_final: 0.8573 (m-30) REVERT: A 226 ILE cc_start: 0.8982 (tp) cc_final: 0.8633 (tp) REVERT: A 230 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7424 (mt-10) REVERT: A 269 ASN cc_start: 0.7577 (m-40) cc_final: 0.7208 (t0) REVERT: E 60 LEU cc_start: 0.9020 (mm) cc_final: 0.8751 (pp) REVERT: E 61 VAL cc_start: 0.9277 (m) cc_final: 0.9075 (p) REVERT: E 63 GLN cc_start: 0.8823 (mt0) cc_final: 0.8550 (mt0) REVERT: E 79 ASN cc_start: 0.8111 (t0) cc_final: 0.7829 (t0) REVERT: E 129 LYS cc_start: 0.9130 (ptpp) cc_final: 0.8909 (mttp) REVERT: E 133 TYR cc_start: 0.8867 (t80) cc_final: 0.8598 (t80) REVERT: E 146 HIS cc_start: 0.7950 (p-80) cc_final: 0.7628 (p90) REVERT: E 203 GLN cc_start: 0.8925 (tp40) cc_final: 0.8559 (tp40) REVERT: E 204 ASP cc_start: 0.8660 (m-30) cc_final: 0.8410 (m-30) REVERT: E 230 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7988 (tm-30) REVERT: E 242 GLN cc_start: 0.7986 (tp40) cc_final: 0.7503 (tp-100) REVERT: E 266 ILE cc_start: 0.8651 (mp) cc_final: 0.8363 (mp) REVERT: E 269 ASN cc_start: 0.7982 (m-40) cc_final: 0.7034 (m-40) REVERT: E 273 GLN cc_start: 0.8674 (mt0) cc_final: 0.8393 (mt0) REVERT: F 79 ASN cc_start: 0.7976 (t0) cc_final: 0.7650 (t0) REVERT: F 95 MET cc_start: 0.8607 (mmm) cc_final: 0.8235 (mmm) REVERT: F 108 PHE cc_start: 0.8981 (p90) cc_final: 0.8149 (p90) REVERT: F 176 GLN cc_start: 0.7671 (tm-30) cc_final: 0.7276 (tm-30) REVERT: F 203 GLN cc_start: 0.8952 (tp40) cc_final: 0.8609 (tp40) REVERT: F 204 ASP cc_start: 0.8930 (m-30) cc_final: 0.8508 (m-30) REVERT: F 226 ILE cc_start: 0.9029 (tp) cc_final: 0.8763 (tp) REVERT: F 227 ARG cc_start: 0.8855 (mmt180) cc_final: 0.8476 (mtt180) REVERT: F 230 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7663 (mt-10) REVERT: F 263 TRP cc_start: 0.8484 (m100) cc_final: 0.7615 (m100) REVERT: F 269 ASN cc_start: 0.7713 (m-40) cc_final: 0.7299 (t0) REVERT: G 46 THR cc_start: 0.8002 (t) cc_final: 0.7534 (p) REVERT: G 79 ASN cc_start: 0.7870 (t0) cc_final: 0.7595 (t0) REVERT: G 108 PHE cc_start: 0.9133 (p90) cc_final: 0.8742 (p90) REVERT: G 140 ASP cc_start: 0.8348 (m-30) cc_final: 0.7925 (t0) REVERT: G 141 ASN cc_start: 0.8803 (t0) cc_final: 0.8418 (t0) REVERT: G 179 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7374 (mt-10) REVERT: G 182 HIS cc_start: 0.8394 (m-70) cc_final: 0.7720 (m170) REVERT: G 183 GLN cc_start: 0.4796 (pm20) cc_final: 0.4567 (pm20) REVERT: G 204 ASP cc_start: 0.8978 (m-30) cc_final: 0.8584 (m-30) REVERT: G 216 LEU cc_start: 0.8744 (tp) cc_final: 0.8496 (mp) REVERT: G 226 ILE cc_start: 0.8929 (tp) cc_final: 0.8666 (tp) REVERT: G 227 ARG cc_start: 0.8794 (mmt180) cc_final: 0.8182 (mtt180) REVERT: G 230 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7785 (mt-10) REVERT: G 238 LEU cc_start: 0.8928 (mt) cc_final: 0.8658 (mt) REVERT: G 241 ILE cc_start: 0.8874 (pt) cc_final: 0.8571 (pt) REVERT: G 242 GLN cc_start: 0.7873 (tp40) cc_final: 0.7510 (tp-100) REVERT: G 260 ASP cc_start: 0.8011 (t0) cc_final: 0.7763 (t0) REVERT: G 261 LEU cc_start: 0.8103 (pt) cc_final: 0.7757 (pt) REVERT: G 269 ASN cc_start: 0.7505 (m-40) cc_final: 0.7051 (m-40) outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.2942 time to fit residues: 183.2826 Evaluate side-chains 399 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 150 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 139 optimal weight: 0.1980 chunk 152 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 D 63 GLN D 228 GLN D 273 GLN A 117 GLN A 228 GLN A 273 GLN E 135 HIS ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN F 228 GLN F 273 GLN G 63 GLN G 135 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.083280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.068126 restraints weight = 45784.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.070965 restraints weight = 26843.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.072983 restraints weight = 18123.413| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.529 16952 Z= 0.259 Angle : 0.948 10.865 23765 Z= 0.359 Chirality : 0.050 0.162 2128 Planarity : 0.005 0.058 2912 Dihedral : 18.083 89.702 2303 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.50 % Favored : 86.50 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.19), residues: 1792 helix: -1.54 (0.28), residues: 287 sheet: -1.26 (0.36), residues: 154 loop : -1.84 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 270 HIS 0.009 0.001 HIS G 276 PHE 0.016 0.002 PHE E 108 TYR 0.015 0.002 TYR B 151 ARG 0.005 0.001 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.03108 ( 154) hydrogen bonds : angle 6.60622 ( 441) covalent geometry : bond 0.00727 (16772) covalent geometry : angle 0.94781 (23765) Misc. bond : bond 0.17621 ( 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 456 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.672 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: B 54 HIS cc_start: 0.7759 (m-70) cc_final: 0.7419 (m-70) REVERT: B 60 LEU cc_start: 0.9198 (mm) cc_final: 0.8952 (mm) REVERT: B 62 GLN cc_start: 0.8693 (mm110) cc_final: 0.8067 (mp10) REVERT: B 63 GLN cc_start: 0.8802 (mt0) cc_final: 0.8396 (mt0) REVERT: B 95 MET cc_start: 0.8428 (mmm) cc_final: 0.8140 (mmm) REVERT: B 117 GLN cc_start: 0.8745 (tp-100) cc_final: 0.8517 (tp40) REVERT: B 129 LYS cc_start: 0.9320 (ptpp) cc_final: 0.9031 (mttp) REVERT: B 146 HIS cc_start: 0.8195 (p90) cc_final: 0.7724 (p90) REVERT: B 148 ILE cc_start: 0.9313 (mm) cc_final: 0.9068 (mm) REVERT: B 183 GLN cc_start: 0.7419 (pm20) cc_final: 0.7155 (pm20) REVERT: B 204 ASP cc_start: 0.8944 (m-30) cc_final: 0.8532 (m-30) REVERT: C 46 THR cc_start: 0.8117 (t) cc_final: 0.7632 (p) REVERT: C 51 LEU cc_start: 0.7529 (mt) cc_final: 0.7313 (mt) REVERT: C 79 ASN cc_start: 0.7964 (t0) cc_final: 0.7653 (t0) REVERT: C 90 THR cc_start: 0.8524 (p) cc_final: 0.8283 (t) REVERT: C 95 MET cc_start: 0.8481 (mmm) cc_final: 0.7800 (mmp) REVERT: C 108 PHE cc_start: 0.8941 (p90) cc_final: 0.8531 (p90) REVERT: C 116 THR cc_start: 0.8857 (m) cc_final: 0.8175 (t) REVERT: C 117 GLN cc_start: 0.8343 (mm-40) cc_final: 0.7991 (mm-40) REVERT: C 141 ASN cc_start: 0.8741 (t0) cc_final: 0.8428 (t0) REVERT: C 179 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7670 (mt-10) REVERT: C 182 HIS cc_start: 0.8392 (m-70) cc_final: 0.7594 (m-70) REVERT: C 183 GLN cc_start: 0.6520 (pm20) cc_final: 0.5997 (pm20) REVERT: C 203 GLN cc_start: 0.9019 (tp40) cc_final: 0.8149 (tp40) REVERT: C 204 ASP cc_start: 0.8819 (m-30) cc_final: 0.8558 (m-30) REVERT: C 238 LEU cc_start: 0.8898 (mp) cc_final: 0.8653 (mt) REVERT: C 260 ASP cc_start: 0.8060 (t0) cc_final: 0.7814 (t0) REVERT: C 261 LEU cc_start: 0.8178 (pt) cc_final: 0.7882 (pt) REVERT: C 269 ASN cc_start: 0.7446 (m-40) cc_final: 0.6879 (m-40) REVERT: C 279 TRP cc_start: 0.7817 (t-100) cc_final: 0.7567 (t-100) REVERT: D 51 LEU cc_start: 0.7629 (mt) cc_final: 0.7386 (mt) REVERT: D 54 HIS cc_start: 0.7516 (m-70) cc_final: 0.7304 (m-70) REVERT: D 197 ARG cc_start: 0.6703 (ttt180) cc_final: 0.6468 (ttt180) REVERT: D 203 GLN cc_start: 0.9033 (tp40) cc_final: 0.8379 (tp40) REVERT: D 204 ASP cc_start: 0.8900 (m-30) cc_final: 0.8584 (m-30) REVERT: D 226 ILE cc_start: 0.9122 (tp) cc_final: 0.8888 (tp) REVERT: D 230 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7713 (mt-10) REVERT: D 238 LEU cc_start: 0.8933 (mt) cc_final: 0.8731 (mt) REVERT: D 242 GLN cc_start: 0.8247 (tp40) cc_final: 0.7814 (tp-100) REVERT: D 269 ASN cc_start: 0.7896 (m-40) cc_final: 0.7502 (m-40) REVERT: A 34 PHE cc_start: 0.8753 (p90) cc_final: 0.8549 (p90) REVERT: A 37 ILE cc_start: 0.8505 (pt) cc_final: 0.8174 (pt) REVERT: A 90 THR cc_start: 0.8530 (p) cc_final: 0.8296 (t) REVERT: A 135 HIS cc_start: 0.7649 (p-80) cc_final: 0.7346 (p-80) REVERT: A 141 ASN cc_start: 0.8705 (t0) cc_final: 0.8391 (t0) REVERT: A 144 ASP cc_start: 0.7878 (p0) cc_final: 0.7434 (p0) REVERT: A 176 GLN cc_start: 0.7743 (tm-30) cc_final: 0.7255 (tm-30) REVERT: A 203 GLN cc_start: 0.8953 (tp40) cc_final: 0.8570 (tp40) REVERT: A 204 ASP cc_start: 0.8858 (m-30) cc_final: 0.8600 (m-30) REVERT: A 230 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7523 (mt-10) REVERT: A 269 ASN cc_start: 0.7712 (m-40) cc_final: 0.7279 (m-40) REVERT: E 51 LEU cc_start: 0.7887 (mt) cc_final: 0.7648 (mt) REVERT: E 54 HIS cc_start: 0.7573 (m-70) cc_final: 0.7366 (m-70) REVERT: E 63 GLN cc_start: 0.8802 (mt0) cc_final: 0.8480 (mt0) REVERT: E 79 ASN cc_start: 0.8161 (t0) cc_final: 0.7840 (t0) REVERT: E 133 TYR cc_start: 0.8850 (t80) cc_final: 0.8521 (t80) REVERT: E 176 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7104 (tm-30) REVERT: E 203 GLN cc_start: 0.8998 (tp40) cc_final: 0.8508 (tp40) REVERT: E 204 ASP cc_start: 0.8673 (m-30) cc_final: 0.8380 (m-30) REVERT: E 213 ASP cc_start: 0.8560 (t0) cc_final: 0.8353 (t0) REVERT: E 216 LEU cc_start: 0.9099 (tt) cc_final: 0.8886 (tt) REVERT: E 242 GLN cc_start: 0.8041 (tp40) cc_final: 0.7655 (tp-100) REVERT: F 51 LEU cc_start: 0.7622 (mt) cc_final: 0.7396 (mt) REVERT: F 79 ASN cc_start: 0.7848 (t0) cc_final: 0.7502 (t0) REVERT: F 95 MET cc_start: 0.8473 (mmm) cc_final: 0.8212 (mmp) REVERT: F 203 GLN cc_start: 0.8964 (tp40) cc_final: 0.8543 (tp40) REVERT: F 204 ASP cc_start: 0.8961 (m-30) cc_final: 0.8501 (m-30) REVERT: F 226 ILE cc_start: 0.9037 (tp) cc_final: 0.8755 (tp) REVERT: F 227 ARG cc_start: 0.8494 (mmt90) cc_final: 0.8214 (mmt90) REVERT: F 230 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7613 (mt-10) REVERT: F 243 LYS cc_start: 0.8856 (tmtt) cc_final: 0.8574 (tptp) REVERT: F 255 LYS cc_start: 0.8761 (pttm) cc_final: 0.8481 (ptpp) REVERT: F 263 TRP cc_start: 0.8591 (m100) cc_final: 0.8161 (m100) REVERT: F 269 ASN cc_start: 0.7706 (m-40) cc_final: 0.7067 (m-40) REVERT: F 279 TRP cc_start: 0.7846 (t-100) cc_final: 0.7591 (t60) REVERT: G 46 THR cc_start: 0.8305 (t) cc_final: 0.7822 (p) REVERT: G 79 ASN cc_start: 0.8036 (t0) cc_final: 0.7729 (t0) REVERT: G 117 GLN cc_start: 0.8384 (mm110) cc_final: 0.8124 (mm110) REVERT: G 141 ASN cc_start: 0.8683 (t0) cc_final: 0.8481 (t0) REVERT: G 179 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7488 (mt-10) REVERT: G 183 GLN cc_start: 0.6653 (pm20) cc_final: 0.6192 (pm20) REVERT: G 204 ASP cc_start: 0.8991 (m-30) cc_final: 0.8576 (m-30) REVERT: G 226 ILE cc_start: 0.8958 (tp) cc_final: 0.8673 (tp) REVERT: G 227 ARG cc_start: 0.8347 (mmt90) cc_final: 0.7985 (mmt90) REVERT: G 230 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7704 (mt-10) REVERT: G 238 LEU cc_start: 0.8897 (mt) cc_final: 0.8552 (mp) REVERT: G 241 ILE cc_start: 0.9016 (pt) cc_final: 0.8659 (pt) REVERT: G 242 GLN cc_start: 0.7939 (tp40) cc_final: 0.7508 (tp-100) REVERT: G 244 ASP cc_start: 0.7976 (t0) cc_final: 0.7591 (t0) REVERT: G 260 ASP cc_start: 0.8100 (t0) cc_final: 0.7827 (t0) REVERT: G 261 LEU cc_start: 0.8189 (pt) cc_final: 0.7827 (pt) REVERT: G 263 TRP cc_start: 0.8402 (m100) cc_final: 0.7898 (m100) REVERT: G 269 ASN cc_start: 0.7595 (m-40) cc_final: 0.7034 (m-40) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.3013 time to fit residues: 197.8157 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 : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 170 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 118 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 HIS B 228 GLN ** 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 63 GLN ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN A 117 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN F 135 HIS F 228 GLN ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN G 135 HIS G 146 HIS ** G 228 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 = 0.3375 r_free = 0.3375 target = 0.084060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.068553 restraints weight = 46160.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.071554 restraints weight = 26268.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.073666 restraints weight = 17402.704| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.517 16952 Z= 0.215 Angle : 0.890 10.021 23765 Z= 0.341 Chirality : 0.048 0.148 2128 Planarity : 0.005 0.051 2912 Dihedral : 18.078 89.337 2303 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.23 % Favored : 86.77 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.20), residues: 1792 helix: -1.75 (0.27), residues: 287 sheet: -1.08 (0.56), residues: 70 loop : -1.52 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 279 HIS 0.009 0.001 HIS E 146 PHE 0.017 0.002 PHE E 103 TYR 0.017 0.002 TYR D 133 ARG 0.002 0.000 ARG B 227 Details of bonding type rmsd hydrogen bonds : bond 0.02909 ( 154) hydrogen bonds : angle 6.51199 ( 441) covalent geometry : bond 0.00602 (16772) covalent geometry : angle 0.88962 (23765) Misc. bond : bond 0.15899 ( 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 467 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 467 time to evaluate : 1.619 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: B 51 LEU cc_start: 0.7622 (mt) cc_final: 0.7418 (mt) REVERT: B 63 GLN cc_start: 0.8875 (mt0) cc_final: 0.8398 (mt0) REVERT: B 95 MET cc_start: 0.8804 (mmm) cc_final: 0.8420 (mmm) REVERT: B 129 LYS cc_start: 0.9275 (ptpp) cc_final: 0.9037 (mttp) REVERT: B 146 HIS cc_start: 0.8169 (p90) cc_final: 0.7712 (p90) REVERT: B 148 ILE cc_start: 0.9256 (mm) cc_final: 0.9034 (mm) REVERT: B 203 GLN cc_start: 0.9040 (tp40) cc_final: 0.8186 (tp40) REVERT: B 227 ARG cc_start: 0.9128 (mtt180) cc_final: 0.8530 (mtt180) REVERT: B 230 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7588 (mt-10) REVERT: C 46 THR cc_start: 0.8229 (t) cc_final: 0.7713 (p) REVERT: C 51 LEU cc_start: 0.7451 (mt) cc_final: 0.7232 (mt) REVERT: C 90 THR cc_start: 0.8498 (p) cc_final: 0.8256 (t) REVERT: C 95 MET cc_start: 0.8525 (mmm) cc_final: 0.8129 (mmm) REVERT: C 108 PHE cc_start: 0.8961 (p90) cc_final: 0.8470 (p90) REVERT: C 135 HIS cc_start: 0.7282 (p90) cc_final: 0.7021 (p-80) REVERT: C 179 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7599 (mt-10) REVERT: C 182 HIS cc_start: 0.8294 (m-70) cc_final: 0.7499 (m-70) REVERT: C 183 GLN cc_start: 0.6289 (pm20) cc_final: 0.5894 (pm20) REVERT: C 203 GLN cc_start: 0.9020 (tp40) cc_final: 0.8163 (tp40) REVERT: C 204 ASP cc_start: 0.8795 (m-30) cc_final: 0.8518 (m-30) REVERT: C 227 ARG cc_start: 0.8727 (mtt180) cc_final: 0.8220 (mtt180) REVERT: C 230 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7720 (mt-10) REVERT: C 238 LEU cc_start: 0.8971 (mp) cc_final: 0.8745 (mt) REVERT: C 269 ASN cc_start: 0.7433 (m-40) cc_final: 0.6778 (m-40) REVERT: C 279 TRP cc_start: 0.7795 (t-100) cc_final: 0.7416 (t-100) REVERT: D 79 ASN cc_start: 0.7976 (t0) cc_final: 0.7674 (t0) REVERT: D 146 HIS cc_start: 0.8144 (p90) cc_final: 0.7666 (p90) REVERT: D 179 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7509 (mt-10) REVERT: D 203 GLN cc_start: 0.9022 (tp40) cc_final: 0.8361 (tp40) REVERT: D 204 ASP cc_start: 0.8892 (m-30) cc_final: 0.8555 (m-30) REVERT: D 213 ASP cc_start: 0.8586 (t0) cc_final: 0.8335 (t0) REVERT: D 227 ARG cc_start: 0.8817 (mmt90) cc_final: 0.8227 (mmt180) REVERT: D 230 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7668 (mt-10) REVERT: D 238 LEU cc_start: 0.8959 (mt) cc_final: 0.8754 (mt) REVERT: D 242 GLN cc_start: 0.8242 (tp40) cc_final: 0.7814 (tp-100) REVERT: D 260 ASP cc_start: 0.8081 (t0) cc_final: 0.7810 (t0) REVERT: D 261 LEU cc_start: 0.8468 (pt) cc_final: 0.8097 (pt) REVERT: D 269 ASN cc_start: 0.7882 (m-40) cc_final: 0.7373 (m-40) REVERT: A 34 PHE cc_start: 0.8747 (p90) cc_final: 0.8547 (p90) REVERT: A 90 THR cc_start: 0.8529 (p) cc_final: 0.8303 (t) REVERT: A 108 PHE cc_start: 0.8876 (p90) cc_final: 0.8675 (p90) REVERT: A 129 LYS cc_start: 0.9242 (ptpp) cc_final: 0.8960 (mttm) REVERT: A 135 HIS cc_start: 0.7736 (p-80) cc_final: 0.7261 (p-80) REVERT: A 176 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7351 (tm-30) REVERT: A 203 GLN cc_start: 0.8949 (tp40) cc_final: 0.8517 (tp40) REVERT: A 204 ASP cc_start: 0.8910 (m-30) cc_final: 0.8649 (m-30) REVERT: A 227 ARG cc_start: 0.8968 (mtt180) cc_final: 0.8293 (mtt180) REVERT: A 230 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7438 (mt-10) REVERT: A 269 ASN cc_start: 0.7784 (m-40) cc_final: 0.7244 (m-40) REVERT: E 51 LEU cc_start: 0.7840 (mt) cc_final: 0.7612 (mt) REVERT: E 54 HIS cc_start: 0.7474 (m-70) cc_final: 0.7150 (m-70) REVERT: E 63 GLN cc_start: 0.8771 (mt0) cc_final: 0.8414 (mt0) REVERT: E 79 ASN cc_start: 0.8142 (t0) cc_final: 0.7794 (t0) REVERT: E 133 TYR cc_start: 0.8852 (t80) cc_final: 0.8469 (t80) REVERT: E 135 HIS cc_start: 0.7852 (p-80) cc_final: 0.7603 (p-80) REVERT: E 176 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7454 (tm-30) REVERT: E 203 GLN cc_start: 0.8957 (tp40) cc_final: 0.8366 (tp40) REVERT: E 204 ASP cc_start: 0.8719 (m-30) cc_final: 0.8374 (m-30) REVERT: E 213 ASP cc_start: 0.8535 (t0) cc_final: 0.8287 (t0) REVERT: E 216 LEU cc_start: 0.9035 (tt) cc_final: 0.8702 (tt) REVERT: E 230 GLU cc_start: 0.8566 (tt0) cc_final: 0.8131 (tt0) REVERT: E 238 LEU cc_start: 0.8997 (mp) cc_final: 0.8776 (mp) REVERT: E 269 ASN cc_start: 0.8132 (m-40) cc_final: 0.7118 (m-40) REVERT: F 51 LEU cc_start: 0.7678 (mt) cc_final: 0.7445 (mt) REVERT: F 79 ASN cc_start: 0.7853 (t0) cc_final: 0.7533 (t0) REVERT: F 95 MET cc_start: 0.8606 (mmm) cc_final: 0.8272 (mmm) REVERT: F 129 LYS cc_start: 0.9180 (mttp) cc_final: 0.8920 (tppt) REVERT: F 135 HIS cc_start: 0.7492 (p90) cc_final: 0.7106 (p90) REVERT: F 176 GLN cc_start: 0.7484 (tm-30) cc_final: 0.7157 (tm-30) REVERT: F 203 GLN cc_start: 0.8963 (tp40) cc_final: 0.8171 (tp40) REVERT: F 204 ASP cc_start: 0.8934 (m-30) cc_final: 0.8540 (m-30) REVERT: F 226 ILE cc_start: 0.9035 (tp) cc_final: 0.8764 (tp) REVERT: F 227 ARG cc_start: 0.8468 (mmt90) cc_final: 0.8205 (mmt90) REVERT: F 230 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7619 (mt-10) REVERT: F 243 LYS cc_start: 0.8799 (tmtt) cc_final: 0.8535 (tptp) REVERT: F 255 LYS cc_start: 0.8814 (pttm) cc_final: 0.8511 (ptpp) REVERT: F 263 TRP cc_start: 0.8538 (m100) cc_final: 0.8073 (m100) REVERT: F 269 ASN cc_start: 0.8154 (m-40) cc_final: 0.7245 (m-40) REVERT: F 279 TRP cc_start: 0.7780 (t-100) cc_final: 0.7569 (t60) REVERT: G 37 ILE cc_start: 0.8305 (pt) cc_final: 0.7742 (mt) REVERT: G 46 THR cc_start: 0.8416 (t) cc_final: 0.7936 (p) REVERT: G 79 ASN cc_start: 0.8087 (t0) cc_final: 0.7742 (t0) REVERT: G 108 PHE cc_start: 0.9053 (p90) cc_final: 0.8569 (p90) REVERT: G 116 THR cc_start: 0.8877 (t) cc_final: 0.8460 (t) REVERT: G 117 GLN cc_start: 0.8369 (mm110) cc_final: 0.8107 (mm110) REVERT: G 135 HIS cc_start: 0.7445 (p90) cc_final: 0.7151 (p90) REVERT: G 179 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7582 (mt-10) REVERT: G 182 HIS cc_start: 0.8123 (m-70) cc_final: 0.7191 (m170) REVERT: G 183 GLN cc_start: 0.6211 (pm20) cc_final: 0.5861 (pm20) REVERT: G 203 GLN cc_start: 0.9110 (tp40) cc_final: 0.8145 (tp40) REVERT: G 204 ASP cc_start: 0.8948 (m-30) cc_final: 0.8516 (m-30) REVERT: G 226 ILE cc_start: 0.8918 (tp) cc_final: 0.8612 (tp) REVERT: G 227 ARG cc_start: 0.8357 (mmt90) cc_final: 0.7949 (mmt90) REVERT: G 230 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7730 (mt-10) REVERT: G 238 LEU cc_start: 0.8920 (mt) cc_final: 0.8659 (mp) REVERT: G 241 ILE cc_start: 0.8948 (pt) cc_final: 0.8405 (pt) REVERT: G 242 GLN cc_start: 0.7948 (tp40) cc_final: 0.7493 (tp-100) REVERT: G 244 ASP cc_start: 0.7986 (t0) cc_final: 0.7680 (t0) REVERT: G 260 ASP cc_start: 0.8161 (t0) cc_final: 0.7926 (t0) REVERT: G 261 LEU cc_start: 0.8110 (pt) cc_final: 0.7782 (pt) REVERT: G 263 TRP cc_start: 0.8339 (m100) cc_final: 0.7909 (m100) REVERT: G 269 ASN cc_start: 0.7590 (m-40) cc_final: 0.7063 (m-40) outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.2924 time to fit residues: 197.6066 Evaluate side-chains 410 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 168 optimal weight: 0.0770 chunk 65 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 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 228 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN F 228 GLN ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 273 GLN G 63 GLN G 146 HIS G 228 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.083468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.068124 restraints weight = 46958.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.071067 restraints weight = 26737.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.073159 restraints weight = 17688.459| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.506 16952 Z= 0.218 Angle : 0.891 9.963 23765 Z= 0.341 Chirality : 0.048 0.147 2128 Planarity : 0.005 0.045 2912 Dihedral : 18.083 89.711 2303 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.90 % Favored : 86.10 % Rotamer: Outliers : 0.06 % Allowed : 3.22 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.20), residues: 1792 helix: -1.78 (0.27), residues: 287 sheet: -1.38 (0.57), residues: 70 loop : -1.50 (0.18), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 270 HIS 0.008 0.001 HIS G 276 PHE 0.025 0.002 PHE F 108 TYR 0.014 0.002 TYR B 151 ARG 0.005 0.001 ARG E 197 Details of bonding type rmsd hydrogen bonds : bond 0.02866 ( 154) hydrogen bonds : angle 6.40634 ( 441) covalent geometry : bond 0.00608 (16772) covalent geometry : angle 0.89054 (23765) Misc. bond : bond 0.16085 ( 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 461 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 460 time to evaluate : 1.589 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 46 THR cc_start: 0.8386 (t) cc_final: 0.7970 (p) REVERT: B 63 GLN cc_start: 0.8806 (mt0) cc_final: 0.8326 (mp10) REVERT: B 79 ASN cc_start: 0.8119 (t0) cc_final: 0.7909 (t0) REVERT: B 95 MET cc_start: 0.8773 (mmm) cc_final: 0.8382 (mmm) REVERT: B 129 LYS cc_start: 0.9250 (ptpp) cc_final: 0.9033 (mttp) REVERT: B 135 HIS cc_start: 0.7551 (p90) cc_final: 0.7343 (p-80) REVERT: B 146 HIS cc_start: 0.8197 (p90) cc_final: 0.7681 (p90) REVERT: B 148 ILE cc_start: 0.9247 (mm) cc_final: 0.8933 (mm) REVERT: B 176 GLN cc_start: 0.7543 (tm-30) cc_final: 0.7290 (tm-30) REVERT: B 203 GLN cc_start: 0.9037 (tp40) cc_final: 0.8339 (tp40) REVERT: B 204 ASP cc_start: 0.8881 (m-30) cc_final: 0.8443 (m-30) REVERT: C 51 LEU cc_start: 0.7335 (mt) cc_final: 0.7128 (mt) REVERT: C 90 THR cc_start: 0.8492 (p) cc_final: 0.8272 (t) REVERT: C 108 PHE cc_start: 0.9027 (p90) cc_final: 0.8491 (p90) REVERT: C 117 GLN cc_start: 0.8323 (mm-40) cc_final: 0.8119 (mm-40) REVERT: C 179 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7547 (mt-10) REVERT: C 182 HIS cc_start: 0.8311 (m-70) cc_final: 0.7526 (m-70) REVERT: C 183 GLN cc_start: 0.6046 (pm20) cc_final: 0.5777 (pm20) REVERT: C 203 GLN cc_start: 0.9005 (tp40) cc_final: 0.8084 (tp40) REVERT: C 204 ASP cc_start: 0.8847 (m-30) cc_final: 0.8526 (m-30) REVERT: C 227 ARG cc_start: 0.8673 (mtt180) cc_final: 0.8154 (mtt180) REVERT: C 230 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7648 (mt-10) REVERT: C 269 ASN cc_start: 0.7427 (m-40) cc_final: 0.6784 (m-40) REVERT: C 279 TRP cc_start: 0.7811 (t-100) cc_final: 0.7553 (t-100) REVERT: D 51 LEU cc_start: 0.7631 (mt) cc_final: 0.7381 (mt) REVERT: D 79 ASN cc_start: 0.8006 (t0) cc_final: 0.7696 (t0) REVERT: D 133 TYR cc_start: 0.8795 (t80) cc_final: 0.8577 (t80) REVERT: D 179 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7568 (mt-10) REVERT: D 203 GLN cc_start: 0.9020 (tp40) cc_final: 0.8342 (tp40) REVERT: D 204 ASP cc_start: 0.8909 (m-30) cc_final: 0.8570 (m-30) REVERT: D 213 ASP cc_start: 0.8714 (t0) cc_final: 0.8443 (t0) REVERT: D 226 ILE cc_start: 0.9151 (tp) cc_final: 0.8883 (tp) REVERT: D 227 ARG cc_start: 0.8670 (mmt90) cc_final: 0.8102 (mmt180) REVERT: D 228 GLN cc_start: 0.8596 (tt0) cc_final: 0.7887 (tm-30) REVERT: D 230 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7683 (mt-10) REVERT: D 238 LEU cc_start: 0.9023 (mt) cc_final: 0.8806 (mt) REVERT: D 242 GLN cc_start: 0.8228 (tp40) cc_final: 0.8008 (tp40) REVERT: D 244 ASP cc_start: 0.8306 (t0) cc_final: 0.8006 (t0) REVERT: D 260 ASP cc_start: 0.8084 (t0) cc_final: 0.7827 (t0) REVERT: D 261 LEU cc_start: 0.8462 (pt) cc_final: 0.8095 (pt) REVERT: D 269 ASN cc_start: 0.7861 (m-40) cc_final: 0.7347 (m-40) REVERT: A 46 THR cc_start: 0.8503 (t) cc_final: 0.8032 (p) REVERT: A 51 LEU cc_start: 0.7834 (mt) cc_final: 0.7561 (mt) REVERT: A 90 THR cc_start: 0.8591 (p) cc_final: 0.8366 (t) REVERT: A 108 PHE cc_start: 0.8907 (p90) cc_final: 0.8695 (p90) REVERT: A 129 LYS cc_start: 0.9247 (ptpp) cc_final: 0.9042 (mttm) REVERT: A 135 HIS cc_start: 0.7941 (p-80) cc_final: 0.7469 (p-80) REVERT: A 176 GLN cc_start: 0.7735 (tm-30) cc_final: 0.7399 (tm-30) REVERT: A 204 ASP cc_start: 0.8888 (m-30) cc_final: 0.8610 (m-30) REVERT: A 227 ARG cc_start: 0.8836 (mtt180) cc_final: 0.8408 (mtt180) REVERT: A 230 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7348 (mt-10) REVERT: A 269 ASN cc_start: 0.7768 (m-40) cc_final: 0.7229 (m-40) REVERT: E 51 LEU cc_start: 0.7824 (mt) cc_final: 0.7604 (mt) REVERT: E 54 HIS cc_start: 0.7543 (m-70) cc_final: 0.7327 (m-70) REVERT: E 60 LEU cc_start: 0.9168 (mm) cc_final: 0.8956 (mm) REVERT: E 63 GLN cc_start: 0.8734 (mt0) cc_final: 0.8401 (mt0) REVERT: E 79 ASN cc_start: 0.8156 (t0) cc_final: 0.7801 (t0) REVERT: E 95 MET cc_start: 0.8869 (mmm) cc_final: 0.8592 (mmm) REVERT: E 133 TYR cc_start: 0.8863 (t80) cc_final: 0.8474 (t80) REVERT: E 135 HIS cc_start: 0.7955 (p-80) cc_final: 0.7641 (p-80) REVERT: E 148 ILE cc_start: 0.9199 (mm) cc_final: 0.8965 (mm) REVERT: E 176 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7603 (tm-30) REVERT: E 203 GLN cc_start: 0.8954 (tp40) cc_final: 0.8316 (tp40) REVERT: E 204 ASP cc_start: 0.8769 (m-30) cc_final: 0.8458 (m-30) REVERT: E 230 GLU cc_start: 0.8591 (tt0) cc_final: 0.8168 (tt0) REVERT: E 261 LEU cc_start: 0.8269 (pt) cc_final: 0.8065 (pt) REVERT: E 269 ASN cc_start: 0.8073 (m-40) cc_final: 0.7092 (m-40) REVERT: E 270 TRP cc_start: 0.8360 (t-100) cc_final: 0.8105 (t-100) REVERT: F 51 LEU cc_start: 0.7638 (mt) cc_final: 0.7418 (mt) REVERT: F 79 ASN cc_start: 0.7900 (t0) cc_final: 0.7556 (t0) REVERT: F 95 MET cc_start: 0.8429 (mmm) cc_final: 0.8207 (mmp) REVERT: F 129 LYS cc_start: 0.9094 (mttp) cc_final: 0.8841 (tppt) REVERT: F 176 GLN cc_start: 0.7510 (tm-30) cc_final: 0.7240 (tm-30) REVERT: F 203 GLN cc_start: 0.9022 (tp40) cc_final: 0.8151 (tp40) REVERT: F 204 ASP cc_start: 0.8931 (m-30) cc_final: 0.8534 (m-30) REVERT: F 226 ILE cc_start: 0.9042 (tp) cc_final: 0.8745 (tp) REVERT: F 227 ARG cc_start: 0.8496 (mmt90) cc_final: 0.8101 (mmt90) REVERT: F 228 GLN cc_start: 0.8659 (tt0) cc_final: 0.8149 (tm-30) REVERT: F 230 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7619 (mt-10) REVERT: F 243 LYS cc_start: 0.8784 (tmtt) cc_final: 0.8526 (tptp) REVERT: F 263 TRP cc_start: 0.8510 (m100) cc_final: 0.8083 (m100) REVERT: F 269 ASN cc_start: 0.7637 (m-40) cc_final: 0.6947 (m-40) REVERT: G 37 ILE cc_start: 0.8170 (pt) cc_final: 0.7626 (mt) REVERT: G 46 THR cc_start: 0.8516 (t) cc_final: 0.7993 (p) REVERT: G 79 ASN cc_start: 0.8182 (t0) cc_final: 0.7840 (t0) REVERT: G 117 GLN cc_start: 0.8339 (mm110) cc_final: 0.8074 (mm110) REVERT: G 141 ASN cc_start: 0.8792 (t0) cc_final: 0.8544 (t0) REVERT: G 179 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7490 (mt-10) REVERT: G 182 HIS cc_start: 0.8072 (m-70) cc_final: 0.7158 (m170) REVERT: G 203 GLN cc_start: 0.9115 (tp40) cc_final: 0.8096 (tp40) REVERT: G 204 ASP cc_start: 0.8940 (m-30) cc_final: 0.8650 (m-30) REVERT: G 226 ILE cc_start: 0.8903 (tp) cc_final: 0.8587 (tp) REVERT: G 230 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7611 (mt-10) REVERT: G 238 LEU cc_start: 0.8882 (mt) cc_final: 0.8577 (mp) REVERT: G 241 ILE cc_start: 0.8990 (pt) cc_final: 0.8405 (pt) REVERT: G 242 GLN cc_start: 0.7967 (tp40) cc_final: 0.7427 (tp-100) REVERT: G 244 ASP cc_start: 0.8086 (t0) cc_final: 0.7794 (t0) REVERT: G 260 ASP cc_start: 0.8153 (t0) cc_final: 0.7906 (t0) REVERT: G 261 LEU cc_start: 0.8100 (pt) cc_final: 0.7780 (pt) REVERT: G 263 TRP cc_start: 0.8342 (m100) cc_final: 0.7977 (m100) REVERT: G 266 ILE cc_start: 0.8609 (mp) cc_final: 0.8324 (mp) outliers start: 1 outliers final: 0 residues processed: 460 average time/residue: 0.2919 time to fit residues: 194.7441 Evaluate side-chains 425 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 0.0470 chunk 23 optimal weight: 0.0010 chunk 126 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 chunk 94 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 114 optimal weight: 0.0980 chunk 119 optimal weight: 0.0870 overall best weight: 0.0620 ------------------------------------------------------------------------------- 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 242 GLN C 146 HIS C 228 GLN C 242 GLN D 63 GLN ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 HIS D 228 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN A 228 GLN A 242 GLN ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 GLN F 63 GLN F 228 GLN F 242 GLN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN G 146 HIS G 228 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.090813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.075395 restraints weight = 44198.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.078626 restraints weight = 24190.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.080884 restraints weight = 15539.689| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.254 16952 Z= 0.136 Angle : 0.838 8.957 23765 Z= 0.327 Chirality : 0.046 0.146 2128 Planarity : 0.004 0.042 2912 Dihedral : 17.829 89.420 2303 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 0.06 % Allowed : 1.74 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.20), residues: 1792 helix: -1.94 (0.27), residues: 294 sheet: None (None), residues: 0 loop : -1.33 (0.17), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 279 HIS 0.007 0.001 HIS D 64 PHE 0.014 0.001 PHE D 103 TYR 0.016 0.002 TYR G 133 ARG 0.002 0.000 ARG E 109 Details of bonding type rmsd hydrogen bonds : bond 0.02878 ( 154) hydrogen bonds : angle 6.58178 ( 441) covalent geometry : bond 0.00349 (16772) covalent geometry : angle 0.83773 (23765) Misc. bond : bond 0.07049 ( 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: 1 poor density : 457 time to evaluate : 1.565 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: B 63 GLN cc_start: 0.8790 (mt0) cc_final: 0.8377 (mp10) REVERT: B 79 ASN cc_start: 0.7931 (t0) cc_final: 0.7576 (t0) REVERT: B 146 HIS cc_start: 0.8110 (p90) cc_final: 0.7725 (p-80) REVERT: B 148 ILE cc_start: 0.9184 (mm) cc_final: 0.8891 (mm) REVERT: B 176 GLN cc_start: 0.7425 (tm-30) cc_final: 0.7092 (tm-30) REVERT: B 200 PHE cc_start: 0.8180 (m-80) cc_final: 0.7171 (m-10) REVERT: B 203 GLN cc_start: 0.9005 (tp40) cc_final: 0.8122 (tp40) REVERT: B 204 ASP cc_start: 0.8717 (m-30) cc_final: 0.7628 (t0) REVERT: B 228 GLN cc_start: 0.8335 (tt0) cc_final: 0.7827 (tm-30) REVERT: B 255 LYS cc_start: 0.8817 (ptpp) cc_final: 0.8598 (ptpp) REVERT: B 277 TRP cc_start: 0.8561 (t-100) cc_final: 0.8342 (t-100) REVERT: C 46 THR cc_start: 0.8032 (t) cc_final: 0.7548 (p) REVERT: C 47 LYS cc_start: 0.8217 (tptm) cc_final: 0.7757 (tptm) REVERT: C 90 THR cc_start: 0.8482 (p) cc_final: 0.8206 (t) REVERT: C 95 MET cc_start: 0.8614 (mmp) cc_final: 0.8363 (mmp) REVERT: C 108 PHE cc_start: 0.8996 (p90) cc_final: 0.8573 (p90) REVERT: C 117 GLN cc_start: 0.8289 (mm-40) cc_final: 0.8069 (mm110) REVERT: C 129 LYS cc_start: 0.9187 (mttt) cc_final: 0.8943 (mmtp) REVERT: C 182 HIS cc_start: 0.7980 (m-70) cc_final: 0.7036 (m170) REVERT: C 203 GLN cc_start: 0.8720 (tp40) cc_final: 0.7759 (tp40) REVERT: C 204 ASP cc_start: 0.8655 (m-30) cc_final: 0.8308 (m-30) REVERT: C 228 GLN cc_start: 0.8478 (tt0) cc_final: 0.7865 (tm-30) REVERT: C 238 LEU cc_start: 0.8952 (mp) cc_final: 0.8673 (mt) REVERT: C 255 LYS cc_start: 0.8660 (ptpp) cc_final: 0.8439 (ptpp) REVERT: C 269 ASN cc_start: 0.7328 (m-40) cc_final: 0.6629 (m-40) REVERT: D 79 ASN cc_start: 0.7776 (t0) cc_final: 0.7388 (t0) REVERT: D 108 PHE cc_start: 0.8856 (p90) cc_final: 0.8575 (p90) REVERT: D 129 LYS cc_start: 0.9218 (mmtp) cc_final: 0.8894 (tppt) REVERT: D 133 TYR cc_start: 0.8625 (t80) cc_final: 0.8420 (t80) REVERT: D 135 HIS cc_start: 0.7450 (p90) cc_final: 0.7165 (p-80) REVERT: D 179 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7283 (mt-10) REVERT: D 183 GLN cc_start: 0.7082 (pm20) cc_final: 0.6426 (pm20) REVERT: D 203 GLN cc_start: 0.8741 (tp40) cc_final: 0.8141 (tp40) REVERT: D 204 ASP cc_start: 0.8759 (m-30) cc_final: 0.8485 (m-30) REVERT: D 213 ASP cc_start: 0.8587 (t0) cc_final: 0.8341 (t0) REVERT: D 226 ILE cc_start: 0.9109 (tp) cc_final: 0.8849 (tp) REVERT: D 230 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7412 (mt-10) REVERT: D 242 GLN cc_start: 0.8226 (tp40) cc_final: 0.7987 (tp40) REVERT: D 260 ASP cc_start: 0.7949 (t0) cc_final: 0.7659 (t0) REVERT: D 261 LEU cc_start: 0.8185 (pt) cc_final: 0.7768 (pt) REVERT: D 269 ASN cc_start: 0.7572 (m-40) cc_final: 0.7046 (m-40) REVERT: A 79 ASN cc_start: 0.7595 (t0) cc_final: 0.7232 (t0) REVERT: A 108 PHE cc_start: 0.8855 (p90) cc_final: 0.8652 (p90) REVERT: A 135 HIS cc_start: 0.7756 (p-80) cc_final: 0.7354 (p-80) REVERT: A 138 PHE cc_start: 0.8572 (m-80) cc_final: 0.8371 (m-80) REVERT: A 176 GLN cc_start: 0.7717 (tm-30) cc_final: 0.7418 (tm-30) REVERT: A 203 GLN cc_start: 0.8633 (tp40) cc_final: 0.8231 (tp40) REVERT: A 226 ILE cc_start: 0.9075 (tp) cc_final: 0.8625 (tp) REVERT: A 227 ARG cc_start: 0.8615 (mtt180) cc_final: 0.8304 (mtt180) REVERT: A 228 GLN cc_start: 0.8497 (tt0) cc_final: 0.8264 (tm-30) REVERT: A 230 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7106 (mt-10) REVERT: A 260 ASP cc_start: 0.7908 (t0) cc_final: 0.7668 (t0) REVERT: A 261 LEU cc_start: 0.8078 (pt) cc_final: 0.7771 (pt) REVERT: A 269 ASN cc_start: 0.7492 (m-40) cc_final: 0.6848 (m-40) REVERT: E 54 HIS cc_start: 0.7308 (m-70) cc_final: 0.7011 (m-70) REVERT: E 63 GLN cc_start: 0.8817 (mt0) cc_final: 0.8424 (mt0) REVERT: E 79 ASN cc_start: 0.8021 (t0) cc_final: 0.7673 (t0) REVERT: E 95 MET cc_start: 0.8785 (mmm) cc_final: 0.8582 (mmm) REVERT: E 108 PHE cc_start: 0.8850 (p90) cc_final: 0.8518 (p90) REVERT: E 129 LYS cc_start: 0.9050 (ptpp) cc_final: 0.8840 (mttp) REVERT: E 133 TYR cc_start: 0.8674 (t80) cc_final: 0.8310 (t80) REVERT: E 135 HIS cc_start: 0.7927 (p-80) cc_final: 0.7550 (p-80) REVERT: E 139 ILE cc_start: 0.9017 (tp) cc_final: 0.8817 (tp) REVERT: E 176 GLN cc_start: 0.7857 (tm-30) cc_final: 0.7653 (tm-30) REVERT: E 203 GLN cc_start: 0.8925 (tp40) cc_final: 0.8362 (tp40) REVERT: E 204 ASP cc_start: 0.8696 (m-30) cc_final: 0.8347 (m-30) REVERT: E 228 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7115 (tm-30) REVERT: E 269 ASN cc_start: 0.8046 (m-40) cc_final: 0.7069 (m-40) REVERT: F 79 ASN cc_start: 0.7614 (t0) cc_final: 0.7351 (t0) REVERT: F 129 LYS cc_start: 0.9094 (mttp) cc_final: 0.8861 (tppt) REVERT: F 176 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7454 (tm-30) REVERT: F 183 GLN cc_start: 0.6728 (pm20) cc_final: 0.6448 (pm20) REVERT: F 203 GLN cc_start: 0.8992 (tp40) cc_final: 0.8300 (tp40) REVERT: F 226 ILE cc_start: 0.8954 (tp) cc_final: 0.8724 (tp) REVERT: F 230 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7576 (mt-10) REVERT: F 243 LYS cc_start: 0.8719 (tmtt) cc_final: 0.8424 (tptp) REVERT: F 263 TRP cc_start: 0.8348 (m100) cc_final: 0.7834 (m100) REVERT: F 269 ASN cc_start: 0.8109 (m-40) cc_final: 0.7173 (m-40) REVERT: F 279 TRP cc_start: 0.7808 (t60) cc_final: 0.7384 (t-100) REVERT: G 46 THR cc_start: 0.8219 (t) cc_final: 0.7443 (p) REVERT: G 79 ASN cc_start: 0.8073 (t0) cc_final: 0.7628 (t0) REVERT: G 149 PRO cc_start: 0.8984 (Cg_exo) cc_final: 0.8716 (Cg_endo) REVERT: G 179 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7131 (mt-10) REVERT: G 182 HIS cc_start: 0.7977 (m-70) cc_final: 0.7165 (m170) REVERT: G 183 GLN cc_start: 0.6385 (pm20) cc_final: 0.5985 (pm20) REVERT: G 203 GLN cc_start: 0.9091 (tp40) cc_final: 0.8153 (tp40) REVERT: G 228 GLN cc_start: 0.8525 (tt0) cc_final: 0.7924 (tm-30) REVERT: G 242 GLN cc_start: 0.8157 (tp40) cc_final: 0.7930 (tp40) REVERT: G 261 LEU cc_start: 0.7752 (pt) cc_final: 0.7478 (pt) REVERT: G 263 TRP cc_start: 0.8061 (m100) cc_final: 0.7782 (m100) outliers start: 1 outliers final: 0 residues processed: 457 average time/residue: 0.2884 time to fit residues: 191.4443 Evaluate side-chains 412 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 411 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 174 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 163 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 123 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.0870 chunk 61 optimal weight: 0.6980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 C 135 HIS C 228 GLN D 54 HIS D 63 GLN D 117 GLN D 146 HIS D 228 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN A 146 HIS ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN A 273 GLN ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN F 117 GLN F 228 GLN F 273 GLN G 54 HIS G 135 HIS G 146 HIS G 228 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.088094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.072804 restraints weight = 45570.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.075920 restraints weight = 25305.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.078104 restraints weight = 16419.944| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.365 16952 Z= 0.160 Angle : 0.845 9.147 23765 Z= 0.329 Chirality : 0.047 0.137 2128 Planarity : 0.004 0.039 2912 Dihedral : 17.712 89.361 2303 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.44 % Favored : 87.56 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.20), residues: 1792 helix: -1.80 (0.26), residues: 294 sheet: None (None), residues: 0 loop : -1.32 (0.17), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 277 HIS 0.006 0.001 HIS A 276 PHE 0.021 0.001 PHE F 108 TYR 0.018 0.002 TYR G 133 ARG 0.004 0.000 ARG E 197 Details of bonding type rmsd hydrogen bonds : bond 0.02903 ( 154) hydrogen bonds : angle 6.68107 ( 441) covalent geometry : bond 0.00458 (16772) covalent geometry : angle 0.84544 (23765) Misc. bond : bond 0.10339 ( 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 452 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 1.489 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: 0.8805 (mt0) cc_final: 0.8373 (mp10) REVERT: B 95 MET cc_start: 0.8670 (mmp) cc_final: 0.8307 (mmp) REVERT: B 108 PHE cc_start: 0.8859 (p90) cc_final: 0.8637 (p90) REVERT: B 146 HIS cc_start: 0.8150 (p90) cc_final: 0.7750 (p-80) REVERT: B 148 ILE cc_start: 0.9199 (mm) cc_final: 0.8955 (mm) REVERT: B 176 GLN cc_start: 0.7286 (tm-30) cc_final: 0.7005 (tm-30) REVERT: B 200 PHE cc_start: 0.8200 (m-80) cc_final: 0.7138 (m-10) REVERT: B 203 GLN cc_start: 0.8871 (tp40) cc_final: 0.8444 (tp40) REVERT: B 204 ASP cc_start: 0.8759 (m-30) cc_final: 0.7681 (t0) REVERT: B 227 ARG cc_start: 0.9162 (mtt180) cc_final: 0.8622 (mtt180) REVERT: B 230 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7542 (mt-10) REVERT: B 255 LYS cc_start: 0.8845 (ptpp) cc_final: 0.8613 (ptpp) REVERT: B 277 TRP cc_start: 0.8541 (t-100) cc_final: 0.8300 (t-100) REVERT: C 46 THR cc_start: 0.8152 (t) cc_final: 0.7630 (p) REVERT: C 90 THR cc_start: 0.8565 (p) cc_final: 0.8308 (t) REVERT: C 95 MET cc_start: 0.8620 (mmp) cc_final: 0.8407 (mmp) REVERT: C 108 PHE cc_start: 0.9049 (p90) cc_final: 0.7838 (p90) REVERT: C 135 HIS cc_start: 0.7524 (p90) cc_final: 0.7000 (p-80) REVERT: C 139 ILE cc_start: 0.8799 (tp) cc_final: 0.8591 (tp) REVERT: C 149 PRO cc_start: 0.8681 (Cg_exo) cc_final: 0.8369 (Cg_endo) REVERT: C 179 GLU cc_start: 0.7772 (tt0) cc_final: 0.6942 (tm-30) REVERT: C 182 HIS cc_start: 0.8341 (m-70) cc_final: 0.8082 (m170) REVERT: C 203 GLN cc_start: 0.8763 (tp40) cc_final: 0.7775 (tp40) REVERT: C 204 ASP cc_start: 0.8678 (m-30) cc_final: 0.8355 (m-30) REVERT: C 227 ARG cc_start: 0.8796 (mtt180) cc_final: 0.8366 (mtt180) REVERT: C 230 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7632 (mt-10) REVERT: C 238 LEU cc_start: 0.8900 (mp) cc_final: 0.8604 (mp) REVERT: C 269 ASN cc_start: 0.7282 (m-40) cc_final: 0.6676 (m-40) REVERT: D 79 ASN cc_start: 0.7911 (t0) cc_final: 0.7559 (t0) REVERT: D 108 PHE cc_start: 0.8921 (p90) cc_final: 0.8560 (p90) REVERT: D 129 LYS cc_start: 0.9228 (mmtp) cc_final: 0.8872 (tppt) REVERT: D 133 TYR cc_start: 0.8676 (t80) cc_final: 0.8454 (t80) REVERT: D 149 PRO cc_start: 0.8966 (Cg_exo) cc_final: 0.7807 (Cg_endo) REVERT: D 179 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7395 (mt-10) REVERT: D 182 HIS cc_start: 0.8080 (m170) cc_final: 0.7201 (m-70) REVERT: D 183 GLN cc_start: 0.7092 (pm20) cc_final: 0.6386 (pm20) REVERT: D 203 GLN cc_start: 0.8766 (tp40) cc_final: 0.8125 (tp40) REVERT: D 204 ASP cc_start: 0.8796 (m-30) cc_final: 0.8485 (m-30) REVERT: D 213 ASP cc_start: 0.8714 (t0) cc_final: 0.8433 (t0) REVERT: D 226 ILE cc_start: 0.9101 (tp) cc_final: 0.8892 (tp) REVERT: D 227 ARG cc_start: 0.8770 (mtt180) cc_final: 0.8306 (mtt180) REVERT: D 228 GLN cc_start: 0.8327 (tt0) cc_final: 0.7750 (tm-30) REVERT: D 230 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7504 (mt-10) REVERT: D 242 GLN cc_start: 0.8264 (tp40) cc_final: 0.7950 (tp40) REVERT: D 260 ASP cc_start: 0.7986 (t0) cc_final: 0.7694 (t0) REVERT: D 261 LEU cc_start: 0.8235 (pt) cc_final: 0.7837 (pt) REVERT: D 269 ASN cc_start: 0.7674 (m-40) cc_final: 0.7152 (m-40) REVERT: D 271 ASP cc_start: 0.7948 (p0) cc_final: 0.7658 (p0) REVERT: A 37 ILE cc_start: 0.8472 (pt) cc_final: 0.8208 (pt) REVERT: A 79 ASN cc_start: 0.7668 (t0) cc_final: 0.7253 (t0) REVERT: A 107 ASP cc_start: 0.8244 (t0) cc_final: 0.7978 (t0) REVERT: A 108 PHE cc_start: 0.8917 (p90) cc_final: 0.8378 (p90) REVERT: A 135 HIS cc_start: 0.7767 (p-80) cc_final: 0.7422 (p90) REVERT: A 176 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7397 (tm-30) REVERT: A 260 ASP cc_start: 0.7935 (t0) cc_final: 0.7714 (t0) REVERT: A 261 LEU cc_start: 0.8165 (pt) cc_final: 0.7903 (pt) REVERT: A 269 ASN cc_start: 0.7596 (m-40) cc_final: 0.7177 (m-40) REVERT: E 54 HIS cc_start: 0.7346 (m-70) cc_final: 0.7048 (m-70) REVERT: E 61 VAL cc_start: 0.9286 (m) cc_final: 0.9084 (p) REVERT: E 63 GLN cc_start: 0.8812 (mt0) cc_final: 0.8401 (mt0) REVERT: E 79 ASN cc_start: 0.8000 (t0) cc_final: 0.7552 (t0) REVERT: E 95 MET cc_start: 0.8786 (mmm) cc_final: 0.8575 (mmm) REVERT: E 108 PHE cc_start: 0.8889 (p90) cc_final: 0.8650 (p90) REVERT: E 129 LYS cc_start: 0.9026 (ptpp) cc_final: 0.8819 (mttp) REVERT: E 130 ASP cc_start: 0.8132 (t0) cc_final: 0.7833 (t0) REVERT: E 133 TYR cc_start: 0.8715 (t80) cc_final: 0.8366 (t80) REVERT: E 135 HIS cc_start: 0.8003 (p-80) cc_final: 0.7603 (p-80) REVERT: E 148 ILE cc_start: 0.9057 (mm) cc_final: 0.8855 (mm) REVERT: E 176 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7436 (tm-30) REVERT: E 203 GLN cc_start: 0.8939 (tp40) cc_final: 0.8329 (tp40) REVERT: E 204 ASP cc_start: 0.8744 (m-30) cc_final: 0.8372 (m-30) REVERT: E 269 ASN cc_start: 0.8066 (m-40) cc_final: 0.7065 (m-40) REVERT: F 54 HIS cc_start: 0.7393 (m-70) cc_final: 0.7125 (m-70) REVERT: F 62 GLN cc_start: 0.8719 (mm110) cc_final: 0.8285 (mm-40) REVERT: F 79 ASN cc_start: 0.7697 (t0) cc_final: 0.7323 (t0) REVERT: F 129 LYS cc_start: 0.9147 (mttp) cc_final: 0.8891 (tppt) REVERT: F 130 ASP cc_start: 0.8080 (t0) cc_final: 0.7843 (t0) REVERT: F 176 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7340 (tm-30) REVERT: F 183 GLN cc_start: 0.6815 (pm20) cc_final: 0.6496 (pm20) REVERT: F 204 ASP cc_start: 0.8852 (m-30) cc_final: 0.8425 (m-30) REVERT: F 226 ILE cc_start: 0.9017 (tp) cc_final: 0.8771 (tp) REVERT: F 228 GLN cc_start: 0.8503 (tt0) cc_final: 0.7909 (tm-30) REVERT: F 230 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7612 (mt-10) REVERT: F 243 LYS cc_start: 0.8747 (tmtt) cc_final: 0.8482 (tptp) REVERT: F 263 TRP cc_start: 0.8389 (m100) cc_final: 0.7961 (m100) REVERT: F 269 ASN cc_start: 0.7667 (m-40) cc_final: 0.6949 (m-40) REVERT: F 279 TRP cc_start: 0.7921 (t60) cc_final: 0.7530 (t60) REVERT: G 34 PHE cc_start: 0.8552 (p90) cc_final: 0.8000 (p90) REVERT: G 46 THR cc_start: 0.8251 (t) cc_final: 0.7664 (p) REVERT: G 79 ASN cc_start: 0.8108 (t0) cc_final: 0.7702 (t0) REVERT: G 108 PHE cc_start: 0.9138 (p90) cc_final: 0.8738 (p90) REVERT: G 141 ASN cc_start: 0.8764 (t0) cc_final: 0.8552 (t0) REVERT: G 149 PRO cc_start: 0.8926 (Cg_exo) cc_final: 0.8553 (Cg_endo) REVERT: G 179 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7306 (mt-10) REVERT: G 182 HIS cc_start: 0.8134 (m-70) cc_final: 0.7434 (m170) REVERT: G 183 GLN cc_start: 0.6277 (pm20) cc_final: 0.6076 (pm20) REVERT: G 203 GLN cc_start: 0.8996 (tp40) cc_final: 0.8577 (tp40) REVERT: G 204 ASP cc_start: 0.8810 (m-30) cc_final: 0.8498 (m-30) REVERT: G 230 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7822 (mt-10) REVERT: G 241 ILE cc_start: 0.8941 (pt) cc_final: 0.8736 (pt) REVERT: G 242 GLN cc_start: 0.8006 (tp40) cc_final: 0.7690 (tp40) REVERT: G 263 TRP cc_start: 0.8144 (m100) cc_final: 0.7855 (m100) REVERT: G 266 ILE cc_start: 0.8706 (mp) cc_final: 0.8483 (mp) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.2910 time to fit residues: 190.3585 Evaluate side-chains 416 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 132 optimal weight: 0.0270 chunk 90 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 154 optimal weight: 0.0070 chunk 159 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 141 optimal weight: 0.0970 chunk 133 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 overall best weight: 0.3854 ------------------------------------------------------------------------------- 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 135 HIS B 228 GLN C 228 GLN D 54 HIS D 135 HIS D 228 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN A 146 HIS A 273 GLN ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN F 228 GLN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN G 117 GLN G 135 HIS G 146 HIS G 228 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.088878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.073710 restraints weight = 45070.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.076837 restraints weight = 24925.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.079030 restraints weight = 16122.028| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.355 16952 Z= 0.155 Angle : 0.832 8.722 23765 Z= 0.326 Chirality : 0.047 0.148 2128 Planarity : 0.004 0.037 2912 Dihedral : 17.627 89.806 2303 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.39 % Favored : 87.61 % 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 : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.20), residues: 1792 helix: -1.82 (0.26), residues: 294 sheet: None (None), residues: 0 loop : -1.37 (0.17), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 279 HIS 0.008 0.001 HIS G 276 PHE 0.010 0.001 PHE B 280 TYR 0.017 0.002 TYR G 133 ARG 0.005 0.001 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.03045 ( 154) hydrogen bonds : angle 6.65869 ( 441) covalent geometry : bond 0.00441 (16772) covalent geometry : angle 0.83161 (23765) Misc. bond : bond 0.09920 ( 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 446 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 1.513 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 63 GLN cc_start: 0.8843 (mt0) cc_final: 0.8365 (mt0) REVERT: B 95 MET cc_start: 0.8631 (mmp) cc_final: 0.8227 (mmp) REVERT: B 109 ARG cc_start: 0.8743 (mmm160) cc_final: 0.8509 (mmm160) REVERT: B 135 HIS cc_start: 0.7468 (p90) cc_final: 0.7255 (p-80) REVERT: B 146 HIS cc_start: 0.8117 (p90) cc_final: 0.7693 (p-80) REVERT: B 148 ILE cc_start: 0.9211 (mm) cc_final: 0.8968 (mm) REVERT: B 149 PRO cc_start: 0.9019 (Cg_exo) cc_final: 0.8678 (Cg_endo) REVERT: B 176 GLN cc_start: 0.7354 (tm-30) cc_final: 0.6993 (tm-30) REVERT: B 200 PHE cc_start: 0.8158 (m-80) cc_final: 0.7108 (m-10) REVERT: B 203 GLN cc_start: 0.8804 (tp40) cc_final: 0.8120 (tp40) REVERT: B 204 ASP cc_start: 0.8759 (m-30) cc_final: 0.7654 (t0) REVERT: B 227 ARG cc_start: 0.9164 (mtt180) cc_final: 0.8586 (mtt180) REVERT: B 228 GLN cc_start: 0.8347 (tt0) cc_final: 0.8133 (tm-30) REVERT: B 230 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7479 (mt-10) REVERT: B 255 LYS cc_start: 0.8859 (ptpp) cc_final: 0.8610 (ptpp) REVERT: B 277 TRP cc_start: 0.8567 (t-100) cc_final: 0.8294 (t-100) REVERT: B 279 TRP cc_start: 0.7707 (t-100) cc_final: 0.7376 (t-100) REVERT: C 46 THR cc_start: 0.8214 (t) cc_final: 0.7913 (t) REVERT: C 90 THR cc_start: 0.8597 (p) cc_final: 0.8340 (t) REVERT: C 95 MET cc_start: 0.8625 (mmp) cc_final: 0.8287 (mmp) REVERT: C 129 LYS cc_start: 0.9278 (mttp) cc_final: 0.8984 (tppt) REVERT: C 135 HIS cc_start: 0.7392 (p90) cc_final: 0.7112 (p-80) REVERT: C 149 PRO cc_start: 0.8594 (Cg_exo) cc_final: 0.8263 (Cg_endo) REVERT: C 176 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7818 (tm-30) REVERT: C 179 GLU cc_start: 0.7642 (tt0) cc_final: 0.6721 (tm-30) REVERT: C 182 HIS cc_start: 0.8329 (m-70) cc_final: 0.7953 (m170) REVERT: C 183 GLN cc_start: 0.5302 (pm20) cc_final: 0.5092 (pm20) REVERT: C 203 GLN cc_start: 0.8738 (tp40) cc_final: 0.7744 (tp40) REVERT: C 204 ASP cc_start: 0.8692 (m-30) cc_final: 0.8358 (m-30) REVERT: C 227 ARG cc_start: 0.8858 (mtt180) cc_final: 0.8248 (mtt180) REVERT: C 228 GLN cc_start: 0.8516 (tt0) cc_final: 0.7890 (tm-30) REVERT: C 230 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7604 (mt-10) REVERT: C 238 LEU cc_start: 0.8885 (mp) cc_final: 0.8572 (mp) REVERT: C 255 LYS cc_start: 0.8716 (ptpp) cc_final: 0.8470 (ptpp) REVERT: C 269 ASN cc_start: 0.7361 (m-40) cc_final: 0.6722 (m-40) REVERT: D 79 ASN cc_start: 0.7905 (t0) cc_final: 0.7556 (t0) REVERT: D 108 PHE cc_start: 0.8971 (p90) cc_final: 0.8500 (p90) REVERT: D 129 LYS cc_start: 0.9199 (mmtp) cc_final: 0.8921 (tppt) REVERT: D 135 HIS cc_start: 0.7392 (p90) cc_final: 0.7166 (p-80) REVERT: D 149 PRO cc_start: 0.8854 (Cg_exo) cc_final: 0.7605 (Cg_endo) REVERT: D 179 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7220 (mt-10) REVERT: D 183 GLN cc_start: 0.6952 (pm20) cc_final: 0.6304 (pm20) REVERT: D 203 GLN cc_start: 0.8757 (tp40) cc_final: 0.8113 (tp40) REVERT: D 204 ASP cc_start: 0.8786 (m-30) cc_final: 0.8418 (m-30) REVERT: D 213 ASP cc_start: 0.8698 (t0) cc_final: 0.8399 (t0) REVERT: D 216 LEU cc_start: 0.9065 (tt) cc_final: 0.8864 (tt) REVERT: D 230 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7476 (mt-10) REVERT: D 242 GLN cc_start: 0.8319 (tp40) cc_final: 0.8008 (tp40) REVERT: D 260 ASP cc_start: 0.8017 (t0) cc_final: 0.7731 (t0) REVERT: D 261 LEU cc_start: 0.8241 (pt) cc_final: 0.7826 (pt) REVERT: D 269 ASN cc_start: 0.7744 (m-40) cc_final: 0.7128 (m-40) REVERT: D 271 ASP cc_start: 0.7879 (p0) cc_final: 0.7651 (p0) REVERT: A 37 ILE cc_start: 0.8477 (pt) cc_final: 0.8193 (pt) REVERT: A 79 ASN cc_start: 0.7671 (t0) cc_final: 0.7299 (t0) REVERT: A 108 PHE cc_start: 0.8950 (p90) cc_final: 0.8674 (p90) REVERT: A 135 HIS cc_start: 0.7761 (p-80) cc_final: 0.7431 (p90) REVERT: A 149 PRO cc_start: 0.8581 (Cg_exo) cc_final: 0.8148 (Cg_endo) REVERT: A 169 ASP cc_start: 0.7101 (t0) cc_final: 0.6786 (p0) REVERT: A 176 GLN cc_start: 0.7680 (tm-30) cc_final: 0.7320 (tm-30) REVERT: A 203 GLN cc_start: 0.8722 (tp40) cc_final: 0.8239 (tp40) REVERT: A 204 ASP cc_start: 0.8853 (m-30) cc_final: 0.8545 (m-30) REVERT: A 260 ASP cc_start: 0.7911 (t0) cc_final: 0.7688 (t0) REVERT: A 261 LEU cc_start: 0.8137 (pt) cc_final: 0.7811 (pt) REVERT: A 269 ASN cc_start: 0.7687 (m-40) cc_final: 0.7092 (m-40) REVERT: E 54 HIS cc_start: 0.7205 (m-70) cc_final: 0.6861 (m-70) REVERT: E 61 VAL cc_start: 0.9268 (m) cc_final: 0.9061 (p) REVERT: E 63 GLN cc_start: 0.8866 (mt0) cc_final: 0.8441 (mt0) REVERT: E 79 ASN cc_start: 0.8035 (t0) cc_final: 0.7632 (t0) REVERT: E 108 PHE cc_start: 0.8835 (p90) cc_final: 0.8600 (p90) REVERT: E 130 ASP cc_start: 0.8133 (t0) cc_final: 0.7829 (t0) REVERT: E 133 TYR cc_start: 0.8673 (t80) cc_final: 0.8357 (t80) REVERT: E 135 HIS cc_start: 0.8000 (p-80) cc_final: 0.7657 (p-80) REVERT: E 148 ILE cc_start: 0.9053 (mm) cc_final: 0.8761 (mm) REVERT: E 176 GLN cc_start: 0.7834 (tm-30) cc_final: 0.7435 (tm-30) REVERT: E 203 GLN cc_start: 0.8927 (tp40) cc_final: 0.8329 (tp40) REVERT: E 204 ASP cc_start: 0.8748 (m-30) cc_final: 0.8389 (m-30) REVERT: E 227 ARG cc_start: 0.8965 (mtt180) cc_final: 0.8569 (mmm160) REVERT: E 230 GLU cc_start: 0.8444 (tt0) cc_final: 0.8022 (tt0) REVERT: E 269 ASN cc_start: 0.8059 (m-40) cc_final: 0.7034 (m-40) REVERT: F 54 HIS cc_start: 0.7388 (m-70) cc_final: 0.7089 (m-70) REVERT: F 79 ASN cc_start: 0.7657 (t0) cc_final: 0.7366 (t0) REVERT: F 109 ARG cc_start: 0.8781 (mmm160) cc_final: 0.8254 (tpp-160) REVERT: F 129 LYS cc_start: 0.9147 (mttp) cc_final: 0.8911 (tppt) REVERT: F 176 GLN cc_start: 0.7204 (tm-30) cc_final: 0.6888 (tm-30) REVERT: F 183 GLN cc_start: 0.6727 (pm20) cc_final: 0.6431 (pm20) REVERT: F 203 GLN cc_start: 0.8816 (tp40) cc_final: 0.8052 (tp40) REVERT: F 204 ASP cc_start: 0.8849 (m-30) cc_final: 0.8400 (m-30) REVERT: F 226 ILE cc_start: 0.8989 (tp) cc_final: 0.8775 (tp) REVERT: F 230 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7619 (mt-10) REVERT: F 243 LYS cc_start: 0.8753 (tmtt) cc_final: 0.8475 (tptp) REVERT: F 263 TRP cc_start: 0.8383 (m100) cc_final: 0.7935 (m100) REVERT: F 269 ASN cc_start: 0.8105 (m-40) cc_final: 0.7213 (m-40) REVERT: F 279 TRP cc_start: 0.7869 (t60) cc_final: 0.7515 (t60) REVERT: G 46 THR cc_start: 0.7726 (t) cc_final: 0.7486 (t) REVERT: G 79 ASN cc_start: 0.8117 (t0) cc_final: 0.7739 (t0) REVERT: G 107 ASP cc_start: 0.8409 (t0) cc_final: 0.7883 (t0) REVERT: G 149 PRO cc_start: 0.8830 (Cg_exo) cc_final: 0.8540 (Cg_endo) REVERT: G 179 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7245 (mt-10) REVERT: G 182 HIS cc_start: 0.8055 (m-70) cc_final: 0.7367 (m170) REVERT: G 203 GLN cc_start: 0.8935 (tp40) cc_final: 0.8472 (tp40) REVERT: G 204 ASP cc_start: 0.8780 (m-30) cc_final: 0.7904 (t0) REVERT: G 227 ARG cc_start: 0.8930 (mtt180) cc_final: 0.8399 (mtt180) REVERT: G 228 GLN cc_start: 0.8536 (tt0) cc_final: 0.7921 (tm-30) REVERT: G 230 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7737 (mt-10) REVERT: G 241 ILE cc_start: 0.8959 (pt) cc_final: 0.8713 (pt) REVERT: G 242 GLN cc_start: 0.8061 (tp40) cc_final: 0.7762 (tp40) REVERT: G 263 TRP cc_start: 0.8172 (m100) cc_final: 0.7855 (m100) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.2918 time to fit residues: 188.0787 Evaluate side-chains 413 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 33 optimal weight: 9.9990 chunk 103 optimal weight: 0.0060 chunk 86 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 130 optimal weight: 0.0060 chunk 113 optimal weight: 1.9990 chunk 170 optimal weight: 0.5980 chunk 19 optimal weight: 0.0030 overall best weight: 0.2622 ------------------------------------------------------------------------------- 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 B 273 GLN C 228 GLN D 117 GLN D 146 HIS D 228 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN F 63 GLN F 228 GLN F 273 GLN G 135 HIS G 146 HIS G 228 GLN ** G 273 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 = 0.3490 r_free = 0.3490 target = 0.090190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.074652 restraints weight = 44741.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.077821 restraints weight = 24685.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.080049 restraints weight = 15974.040| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.339 16952 Z= 0.144 Angle : 0.825 8.619 23765 Z= 0.324 Chirality : 0.046 0.145 2128 Planarity : 0.005 0.049 2912 Dihedral : 17.523 89.324 2303 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.72 % Favored : 88.28 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.20), residues: 1792 helix: -1.74 (0.26), residues: 294 sheet: None (None), residues: 0 loop : -1.35 (0.17), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 279 HIS 0.006 0.001 HIS G 276 PHE 0.022 0.001 PHE C 108 TYR 0.016 0.002 TYR G 133 ARG 0.004 0.001 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.02988 ( 154) hydrogen bonds : angle 6.65072 ( 441) covalent geometry : bond 0.00401 (16772) covalent geometry : angle 0.82492 (23765) Misc. bond : bond 0.08857 ( 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 440 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 1.491 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: symmetry clash REVERT: B 60 LEU cc_start: 0.8955 (pp) cc_final: 0.8672 (pp) REVERT: B 63 GLN cc_start: 0.8730 (mt0) cc_final: 0.8261 (mp10) REVERT: B 79 ASN cc_start: 0.7948 (t0) cc_final: 0.7619 (t0) REVERT: B 95 MET cc_start: 0.8640 (mmp) cc_final: 0.8310 (mmp) REVERT: B 117 GLN cc_start: 0.8841 (tp40) cc_final: 0.8539 (tp-100) REVERT: B 135 HIS cc_start: 0.7343 (p90) cc_final: 0.7017 (p-80) REVERT: B 146 HIS cc_start: 0.8018 (p-80) cc_final: 0.7753 (p-80) REVERT: B 148 ILE cc_start: 0.9190 (mm) cc_final: 0.8930 (mm) REVERT: B 149 PRO cc_start: 0.8944 (Cg_exo) cc_final: 0.8570 (Cg_endo) REVERT: B 176 GLN cc_start: 0.7246 (tm-30) cc_final: 0.6927 (tm-30) REVERT: B 200 PHE cc_start: 0.8095 (m-80) cc_final: 0.7027 (m-10) REVERT: B 203 GLN cc_start: 0.8805 (tp40) cc_final: 0.8189 (tp40) REVERT: B 204 ASP cc_start: 0.8713 (m-30) cc_final: 0.7599 (t0) REVERT: B 227 ARG cc_start: 0.9126 (mtt180) cc_final: 0.8578 (mtt180) REVERT: B 230 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7495 (mt-10) REVERT: B 255 LYS cc_start: 0.8892 (ptpp) cc_final: 0.8637 (ptpp) REVERT: B 277 TRP cc_start: 0.8553 (t-100) cc_final: 0.8294 (t-100) REVERT: B 279 TRP cc_start: 0.7624 (t-100) cc_final: 0.7292 (t-100) REVERT: C 90 THR cc_start: 0.8605 (p) cc_final: 0.8344 (t) REVERT: C 95 MET cc_start: 0.8632 (mmp) cc_final: 0.8341 (mmp) REVERT: C 108 PHE cc_start: 0.8579 (p90) cc_final: 0.8366 (p90) REVERT: C 135 HIS cc_start: 0.7329 (p90) cc_final: 0.7087 (p-80) REVERT: C 139 ILE cc_start: 0.8780 (tp) cc_final: 0.8578 (tp) REVERT: C 149 PRO cc_start: 0.8484 (Cg_exo) cc_final: 0.7943 (Cg_endo) REVERT: C 179 GLU cc_start: 0.7595 (tt0) cc_final: 0.6598 (tm-30) REVERT: C 182 HIS cc_start: 0.8328 (m-70) cc_final: 0.7945 (m170) REVERT: C 200 PHE cc_start: 0.7759 (m-80) cc_final: 0.6902 (m-10) REVERT: C 203 GLN cc_start: 0.8736 (tp40) cc_final: 0.7720 (tp40) REVERT: C 204 ASP cc_start: 0.8660 (m-30) cc_final: 0.7654 (t0) REVERT: C 227 ARG cc_start: 0.8720 (mtt180) cc_final: 0.8447 (mtt180) REVERT: C 230 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7507 (mt-10) REVERT: C 238 LEU cc_start: 0.8918 (mp) cc_final: 0.8626 (mp) REVERT: C 243 LYS cc_start: 0.8594 (tmtt) cc_final: 0.8378 (tptp) REVERT: C 255 LYS cc_start: 0.8745 (ptpp) cc_final: 0.8482 (ptpp) REVERT: C 263 TRP cc_start: 0.8163 (m100) cc_final: 0.7866 (m100) REVERT: C 269 ASN cc_start: 0.7360 (m-40) cc_final: 0.6754 (m-40) REVERT: D 46 THR cc_start: 0.7463 (t) cc_final: 0.7134 (t) REVERT: D 79 ASN cc_start: 0.7923 (t0) cc_final: 0.7538 (t0) REVERT: D 108 PHE cc_start: 0.8989 (p90) cc_final: 0.8562 (p90) REVERT: D 129 LYS cc_start: 0.9193 (mmtp) cc_final: 0.8888 (tppt) REVERT: D 179 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7153 (mt-10) REVERT: D 182 HIS cc_start: 0.7959 (m170) cc_final: 0.6975 (m-70) REVERT: D 183 GLN cc_start: 0.6886 (pm20) cc_final: 0.6264 (pm20) REVERT: D 203 GLN cc_start: 0.8746 (tp40) cc_final: 0.8090 (tp40) REVERT: D 204 ASP cc_start: 0.8700 (m-30) cc_final: 0.8339 (m-30) REVERT: D 213 ASP cc_start: 0.8695 (t0) cc_final: 0.8395 (t0) REVERT: D 226 ILE cc_start: 0.9124 (tp) cc_final: 0.8916 (tp) REVERT: D 227 ARG cc_start: 0.8843 (mtt180) cc_final: 0.8412 (mtt180) REVERT: D 228 GLN cc_start: 0.8105 (tt0) cc_final: 0.7570 (tm-30) REVERT: D 230 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7389 (mt-10) REVERT: D 242 GLN cc_start: 0.8325 (tp40) cc_final: 0.8102 (tp40) REVERT: D 260 ASP cc_start: 0.7971 (t0) cc_final: 0.7768 (t0) REVERT: D 261 LEU cc_start: 0.8201 (pt) cc_final: 0.7880 (pt) REVERT: D 269 ASN cc_start: 0.7713 (m-40) cc_final: 0.7183 (m-40) REVERT: D 271 ASP cc_start: 0.7807 (p0) cc_final: 0.7582 (p0) REVERT: A 54 HIS cc_start: 0.7592 (m-70) cc_final: 0.7093 (m-70) REVERT: A 79 ASN cc_start: 0.7573 (t0) cc_final: 0.7130 (t0) REVERT: A 108 PHE cc_start: 0.8919 (p90) cc_final: 0.8689 (p90) REVERT: A 135 HIS cc_start: 0.7724 (p-80) cc_final: 0.7437 (p90) REVERT: A 169 ASP cc_start: 0.7020 (t0) cc_final: 0.6710 (p0) REVERT: A 176 GLN cc_start: 0.7434 (tm-30) cc_final: 0.7193 (tm-30) REVERT: A 203 GLN cc_start: 0.8716 (tp40) cc_final: 0.8261 (tp40) REVERT: A 204 ASP cc_start: 0.8831 (m-30) cc_final: 0.8521 (m-30) REVERT: A 227 ARG cc_start: 0.8913 (mtt180) cc_final: 0.8170 (mtt180) REVERT: A 230 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7288 (mt-10) REVERT: A 260 ASP cc_start: 0.7894 (t0) cc_final: 0.7661 (t0) REVERT: A 261 LEU cc_start: 0.8057 (pt) cc_final: 0.7754 (pt) REVERT: A 269 ASN cc_start: 0.8015 (m-40) cc_final: 0.7195 (m-40) REVERT: A 271 ASP cc_start: 0.7883 (p0) cc_final: 0.7659 (p0) REVERT: E 61 VAL cc_start: 0.9215 (m) cc_final: 0.9002 (p) REVERT: E 63 GLN cc_start: 0.8828 (mt0) cc_final: 0.8414 (mt0) REVERT: E 79 ASN cc_start: 0.7934 (t0) cc_final: 0.7426 (t0) REVERT: E 108 PHE cc_start: 0.8858 (p90) cc_final: 0.8602 (p90) REVERT: E 109 ARG cc_start: 0.8918 (mmm160) cc_final: 0.8662 (mmt180) REVERT: E 129 LYS cc_start: 0.9153 (mttp) cc_final: 0.8847 (mmtp) REVERT: E 130 ASP cc_start: 0.8021 (t0) cc_final: 0.7739 (t0) REVERT: E 133 TYR cc_start: 0.8610 (t80) cc_final: 0.8294 (t80) REVERT: E 135 HIS cc_start: 0.7918 (p-80) cc_final: 0.7549 (p-80) REVERT: E 148 ILE cc_start: 0.9041 (mm) cc_final: 0.8705 (mm) REVERT: E 176 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7388 (tm-30) REVERT: E 203 GLN cc_start: 0.8952 (tp40) cc_final: 0.8351 (tp40) REVERT: E 204 ASP cc_start: 0.8724 (m-30) cc_final: 0.8339 (m-30) REVERT: E 227 ARG cc_start: 0.8935 (mtt180) cc_final: 0.8592 (mmt180) REVERT: E 230 GLU cc_start: 0.8438 (tt0) cc_final: 0.7974 (tt0) REVERT: E 269 ASN cc_start: 0.8035 (m-40) cc_final: 0.6928 (m-40) REVERT: F 79 ASN cc_start: 0.7628 (t0) cc_final: 0.7310 (t0) REVERT: F 109 ARG cc_start: 0.8757 (mmm160) cc_final: 0.8154 (tpp-160) REVERT: F 129 LYS cc_start: 0.9166 (mttp) cc_final: 0.8925 (tppt) REVERT: F 130 ASP cc_start: 0.8065 (t0) cc_final: 0.7830 (t0) REVERT: F 176 GLN cc_start: 0.7403 (tm-30) cc_final: 0.6915 (tm-30) REVERT: F 183 GLN cc_start: 0.6648 (pm20) cc_final: 0.6322 (pm20) REVERT: F 203 GLN cc_start: 0.8824 (tp40) cc_final: 0.8108 (tp40) REVERT: F 204 ASP cc_start: 0.8782 (m-30) cc_final: 0.8285 (m-30) REVERT: F 227 ARG cc_start: 0.8915 (mtt180) cc_final: 0.8385 (mmt90) REVERT: F 228 GLN cc_start: 0.8432 (tt0) cc_final: 0.8071 (tm-30) REVERT: F 230 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7646 (mt-10) REVERT: F 243 LYS cc_start: 0.8752 (tmtt) cc_final: 0.8484 (tptp) REVERT: F 263 TRP cc_start: 0.8335 (m100) cc_final: 0.7905 (m100) REVERT: F 269 ASN cc_start: 0.7622 (m-40) cc_final: 0.6978 (m-40) REVERT: F 279 TRP cc_start: 0.7807 (t60) cc_final: 0.7493 (t60) REVERT: G 46 THR cc_start: 0.7851 (t) cc_final: 0.7042 (p) REVERT: G 79 ASN cc_start: 0.8124 (t0) cc_final: 0.7735 (t0) REVERT: G 149 PRO cc_start: 0.8814 (Cg_exo) cc_final: 0.8471 (Cg_endo) REVERT: G 179 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7155 (mt-10) REVERT: G 182 HIS cc_start: 0.8125 (m-70) cc_final: 0.7375 (m170) REVERT: G 183 GLN cc_start: 0.7133 (pm20) cc_final: 0.6795 (pm20) REVERT: G 200 PHE cc_start: 0.8189 (m-80) cc_final: 0.7720 (m-10) REVERT: G 203 GLN cc_start: 0.8928 (tp40) cc_final: 0.7877 (tp40) REVERT: G 204 ASP cc_start: 0.8732 (m-30) cc_final: 0.7854 (t0) REVERT: G 227 ARG cc_start: 0.8889 (mtt180) cc_final: 0.8299 (mtt180) REVERT: G 230 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7697 (mt-10) REVERT: G 241 ILE cc_start: 0.8960 (pt) cc_final: 0.8740 (pt) REVERT: G 242 GLN cc_start: 0.8094 (tp40) cc_final: 0.7798 (tp40) REVERT: G 243 LYS cc_start: 0.8566 (tmtt) cc_final: 0.8277 (tptp) REVERT: G 266 ILE cc_start: 0.8736 (mp) cc_final: 0.8517 (mp) outliers start: 0 outliers final: 0 residues processed: 440 average time/residue: 0.2853 time to fit residues: 180.9808 Evaluate side-chains 411 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 154 optimal weight: 0.3980 chunk 47 optimal weight: 4.9990 chunk 163 optimal weight: 0.0570 chunk 83 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 228 GLN D 117 GLN D 135 HIS D 228 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN A 146 HIS ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN F 63 GLN F 228 GLN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN G 117 GLN ** G 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 HIS G 228 GLN ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.087603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.072417 restraints weight = 45886.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.075485 restraints weight = 25658.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077627 restraints weight = 16749.460| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.426 16952 Z= 0.183 Angle : 0.865 11.185 23765 Z= 0.338 Chirality : 0.048 0.148 2128 Planarity : 0.005 0.065 2912 Dihedral : 17.755 89.798 2303 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.44 % Favored : 87.56 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.20), residues: 1792 helix: -1.79 (0.27), residues: 294 sheet: -2.24 (0.56), residues: 70 loop : -1.52 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 277 HIS 0.008 0.001 HIS G 276 PHE 0.023 0.002 PHE C 108 TYR 0.016 0.002 TYR G 133 ARG 0.005 0.001 ARG C 109 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 154) hydrogen bonds : angle 6.78232 ( 441) covalent geometry : bond 0.00524 (16772) covalent geometry : angle 0.86524 (23765) Misc. bond : bond 0.12027 ( 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 448 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 1.630 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 60 LEU cc_start: 0.9016 (pp) cc_final: 0.8712 (pp) REVERT: B 63 GLN cc_start: 0.8754 (mt0) cc_final: 0.8360 (mp10) REVERT: B 95 MET cc_start: 0.8625 (mmp) cc_final: 0.8213 (mmp) REVERT: B 146 HIS cc_start: 0.8077 (p-80) cc_final: 0.7693 (p90) REVERT: B 148 ILE cc_start: 0.9187 (mm) cc_final: 0.8879 (mm) REVERT: B 149 PRO cc_start: 0.8999 (Cg_exo) cc_final: 0.8696 (Cg_endo) REVERT: B 151 TYR cc_start: 0.8852 (p90) cc_final: 0.8623 (p90) REVERT: B 176 GLN cc_start: 0.7174 (tm-30) cc_final: 0.6609 (tm-30) REVERT: B 179 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7601 (mt-10) REVERT: B 200 PHE cc_start: 0.8089 (m-80) cc_final: 0.7817 (m-10) REVERT: B 203 GLN cc_start: 0.8761 (tp40) cc_final: 0.8292 (tp40) REVERT: B 204 ASP cc_start: 0.8774 (m-30) cc_final: 0.7807 (t0) REVERT: B 227 ARG cc_start: 0.9128 (mtt180) cc_final: 0.8499 (mtt180) REVERT: B 230 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7483 (mt-10) REVERT: B 255 LYS cc_start: 0.8861 (ptpp) cc_final: 0.8616 (ptpp) REVERT: B 277 TRP cc_start: 0.8559 (t-100) cc_final: 0.8209 (t-100) REVERT: B 279 TRP cc_start: 0.7730 (t-100) cc_final: 0.7436 (t-100) REVERT: C 46 THR cc_start: 0.7865 (t) cc_final: 0.7601 (t) REVERT: C 62 GLN cc_start: 0.8818 (mm110) cc_final: 0.8329 (mm110) REVERT: C 90 THR cc_start: 0.8591 (p) cc_final: 0.8351 (t) REVERT: C 95 MET cc_start: 0.8657 (mmp) cc_final: 0.8362 (mmp) REVERT: C 149 PRO cc_start: 0.8634 (Cg_exo) cc_final: 0.8290 (Cg_endo) REVERT: C 179 GLU cc_start: 0.7487 (tt0) cc_final: 0.6638 (tm-30) REVERT: C 203 GLN cc_start: 0.8771 (tp40) cc_final: 0.7750 (tp40) REVERT: C 204 ASP cc_start: 0.8754 (m-30) cc_final: 0.8388 (m-30) REVERT: C 227 ARG cc_start: 0.8758 (mtt180) cc_final: 0.8242 (mtt180) REVERT: C 228 GLN cc_start: 0.8450 (tt0) cc_final: 0.8040 (tm-30) REVERT: C 230 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7637 (mt-10) REVERT: C 238 LEU cc_start: 0.8927 (mp) cc_final: 0.8679 (mt) REVERT: C 255 LYS cc_start: 0.8759 (ptpp) cc_final: 0.8460 (ptpp) REVERT: C 269 ASN cc_start: 0.7385 (m-40) cc_final: 0.6827 (m-40) REVERT: D 46 THR cc_start: 0.7727 (t) cc_final: 0.7389 (t) REVERT: D 79 ASN cc_start: 0.7974 (t0) cc_final: 0.7632 (t0) REVERT: D 107 ASP cc_start: 0.8493 (t0) cc_final: 0.8194 (t0) REVERT: D 108 PHE cc_start: 0.9008 (p90) cc_final: 0.8585 (p90) REVERT: D 109 ARG cc_start: 0.9103 (mmt90) cc_final: 0.8878 (mmt90) REVERT: D 129 LYS cc_start: 0.9195 (mmtp) cc_final: 0.8887 (tppt) REVERT: D 133 TYR cc_start: 0.8636 (t80) cc_final: 0.8426 (t80) REVERT: D 149 PRO cc_start: 0.8926 (Cg_exo) cc_final: 0.7855 (Cg_endo) REVERT: D 179 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7209 (mt-10) REVERT: D 182 HIS cc_start: 0.8030 (m170) cc_final: 0.7079 (m-70) REVERT: D 183 GLN cc_start: 0.6916 (pm20) cc_final: 0.6297 (pm20) REVERT: D 203 GLN cc_start: 0.8794 (tp40) cc_final: 0.8112 (tp40) REVERT: D 204 ASP cc_start: 0.8770 (m-30) cc_final: 0.8357 (m-30) REVERT: D 213 ASP cc_start: 0.8688 (t0) cc_final: 0.8383 (t0) REVERT: D 227 ARG cc_start: 0.8857 (mtt180) cc_final: 0.8557 (mtt180) REVERT: D 230 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7509 (mt-10) REVERT: D 238 LEU cc_start: 0.8944 (mt) cc_final: 0.8704 (mt) REVERT: D 261 LEU cc_start: 0.8154 (pt) cc_final: 0.7865 (pt) REVERT: D 269 ASN cc_start: 0.7793 (m-40) cc_final: 0.7219 (m-40) REVERT: A 37 ILE cc_start: 0.8436 (pt) cc_final: 0.8225 (pt) REVERT: A 54 HIS cc_start: 0.7673 (m-70) cc_final: 0.7137 (m-70) REVERT: A 79 ASN cc_start: 0.7642 (t0) cc_final: 0.7213 (t0) REVERT: A 95 MET cc_start: 0.8990 (mmp) cc_final: 0.8753 (mmm) REVERT: A 108 PHE cc_start: 0.8972 (p90) cc_final: 0.8646 (p90) REVERT: A 135 HIS cc_start: 0.7803 (p-80) cc_final: 0.7510 (p90) REVERT: A 169 ASP cc_start: 0.7167 (t0) cc_final: 0.6720 (p0) REVERT: A 204 ASP cc_start: 0.8889 (m-30) cc_final: 0.8588 (m-30) REVERT: A 228 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7947 (tm-30) REVERT: A 260 ASP cc_start: 0.7949 (t0) cc_final: 0.7729 (t0) REVERT: A 261 LEU cc_start: 0.8172 (pt) cc_final: 0.7887 (pt) REVERT: A 269 ASN cc_start: 0.7677 (m-40) cc_final: 0.7071 (m-40) REVERT: E 63 GLN cc_start: 0.8906 (mt0) cc_final: 0.8470 (mt0) REVERT: E 79 ASN cc_start: 0.7934 (t0) cc_final: 0.7487 (t0) REVERT: E 108 PHE cc_start: 0.8913 (p90) cc_final: 0.8600 (p90) REVERT: E 129 LYS cc_start: 0.9104 (mttp) cc_final: 0.8783 (mmtp) REVERT: E 130 ASP cc_start: 0.8011 (t0) cc_final: 0.7652 (t0) REVERT: E 133 TYR cc_start: 0.8731 (t80) cc_final: 0.8406 (t80) REVERT: E 135 HIS cc_start: 0.7996 (p-80) cc_final: 0.7766 (p90) REVERT: E 148 ILE cc_start: 0.9111 (mm) cc_final: 0.8641 (mm) REVERT: E 176 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7292 (tm-30) REVERT: E 203 GLN cc_start: 0.8929 (tp40) cc_final: 0.8298 (tp40) REVERT: E 204 ASP cc_start: 0.8771 (m-30) cc_final: 0.8388 (m-30) REVERT: E 230 GLU cc_start: 0.8511 (tt0) cc_final: 0.7962 (tt0) REVERT: E 269 ASN cc_start: 0.8036 (m-40) cc_final: 0.7302 (m-40) REVERT: F 79 ASN cc_start: 0.7740 (t0) cc_final: 0.7482 (t0) REVERT: F 106 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8515 (tm-30) REVERT: F 129 LYS cc_start: 0.9149 (mttp) cc_final: 0.8912 (tppt) REVERT: F 130 ASP cc_start: 0.8078 (t0) cc_final: 0.7869 (t0) REVERT: F 176 GLN cc_start: 0.7220 (tm-30) cc_final: 0.6773 (tm-30) REVERT: F 179 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7650 (mt-10) REVERT: F 183 GLN cc_start: 0.6626 (pm20) cc_final: 0.6317 (pm20) REVERT: F 203 GLN cc_start: 0.8841 (tp40) cc_final: 0.7924 (tp40) REVERT: F 204 ASP cc_start: 0.8853 (m-30) cc_final: 0.8376 (m-30) REVERT: F 227 ARG cc_start: 0.8948 (mtt180) cc_final: 0.8119 (mmm160) REVERT: F 228 GLN cc_start: 0.8276 (tt0) cc_final: 0.7931 (tm-30) REVERT: F 230 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7773 (mt-10) REVERT: F 243 LYS cc_start: 0.8781 (tmtt) cc_final: 0.8481 (tptp) REVERT: F 263 TRP cc_start: 0.8391 (m100) cc_final: 0.7917 (m100) REVERT: F 269 ASN cc_start: 0.8153 (m-40) cc_final: 0.7310 (m-40) REVERT: G 34 PHE cc_start: 0.8588 (p90) cc_final: 0.8204 (p90) REVERT: G 37 ILE cc_start: 0.8425 (pt) cc_final: 0.7898 (mt) REVERT: G 46 THR cc_start: 0.8116 (t) cc_final: 0.7297 (p) REVERT: G 54 HIS cc_start: 0.7620 (m-70) cc_final: 0.7335 (m-70) REVERT: G 141 ASN cc_start: 0.8811 (t0) cc_final: 0.8562 (t0) REVERT: G 149 PRO cc_start: 0.8896 (Cg_exo) cc_final: 0.8513 (Cg_endo) REVERT: G 179 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7082 (mt-10) REVERT: G 182 HIS cc_start: 0.8144 (m-70) cc_final: 0.7392 (m170) REVERT: G 183 GLN cc_start: 0.6738 (pm20) cc_final: 0.6518 (pm20) REVERT: G 200 PHE cc_start: 0.8257 (m-80) cc_final: 0.7743 (m-10) REVERT: G 203 GLN cc_start: 0.8976 (tp40) cc_final: 0.7826 (tp40) REVERT: G 204 ASP cc_start: 0.8778 (m-30) cc_final: 0.7857 (t0) REVERT: G 213 ASP cc_start: 0.8660 (t0) cc_final: 0.8450 (t0) REVERT: G 228 GLN cc_start: 0.8453 (tt0) cc_final: 0.7837 (tm-30) REVERT: G 230 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7802 (mt-10) REVERT: G 243 LYS cc_start: 0.8657 (tmtt) cc_final: 0.8211 (tptp) REVERT: G 269 ASN cc_start: 0.7704 (m-40) cc_final: 0.7121 (m-40) outliers start: 0 outliers final: 0 residues processed: 448 average time/residue: 0.2990 time to fit residues: 194.3594 Evaluate side-chains 416 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 72 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 74 optimal weight: 0.0370 chunk 60 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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** C 135 HIS C 228 GLN D 135 HIS D 146 HIS D 228 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN F 63 GLN F 273 GLN ** G 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 HIS G 228 GLN ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.085853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.070826 restraints weight = 46281.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.073817 restraints weight = 25804.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.075940 restraints weight = 16828.877| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 0.484 16952 Z= 0.198 Angle : 0.876 10.022 23765 Z= 0.339 Chirality : 0.048 0.143 2128 Planarity : 0.005 0.062 2912 Dihedral : 17.931 89.367 2303 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.20), residues: 1792 helix: -1.86 (0.26), residues: 294 sheet: -2.33 (0.55), residues: 70 loop : -1.60 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 279 HIS 0.009 0.001 HIS G 276 PHE 0.022 0.002 PHE F 108 TYR 0.016 0.002 TYR G 133 ARG 0.005 0.001 ARG E 197 Details of bonding type rmsd hydrogen bonds : bond 0.02985 ( 154) hydrogen bonds : angle 6.90695 ( 441) covalent geometry : bond 0.00565 (16772) covalent geometry : angle 0.87631 (23765) Misc. bond : bond 0.13580 ( 180) =============================================================================== Job complete usr+sys time: 5912.68 seconds wall clock time: 102 minutes 55.61 seconds (6175.61 seconds total)