Starting phenix.real_space_refine on Sat May 17 16:07:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d9m_27266/05_2025/8d9m_27266.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d9m_27266/05_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_27266/05_2025/8d9m_27266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d9m_27266/05_2025/8d9m_27266.map" model { file = "/net/cci-nas-00/data/ceres_data/8d9m_27266/05_2025/8d9m_27266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d9m_27266/05_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-5687/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: 5.60, per 1000 atoms: 0.35 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: 4.54 Conformation dependent library (CDL) restraints added in 1.7 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: 1.16 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: 3.18 Time building geometry restraints manager: 5.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 6902 1.39 - 1.56: 9499 1.56 - 1.73: 7 1.73 - 1.90: 140 1.90 - 2.08: 224 Bond restraints: 16772 Sorted by residual: bond pdb=" CA ALA G 89 " pdb=" C ALA G 89 " ideal model delta sigma weight residual 1.524 1.484 0.040 1.48e-02 4.57e+03 7.33e+00 bond pdb=" CA ALA C 89 " pdb=" C ALA C 89 " ideal model delta sigma weight residual 1.524 1.485 0.040 1.48e-02 4.57e+03 7.27e+00 bond pdb=" CA ALA E 89 " pdb=" C ALA E 89 " ideal model delta sigma weight residual 1.524 1.485 0.040 1.48e-02 4.57e+03 7.22e+00 bond pdb=" CA ALA B 89 " pdb=" C ALA B 89 " ideal model delta sigma weight residual 1.524 1.485 0.040 1.48e-02 4.57e+03 7.17e+00 bond pdb=" CA ALA A 89 " pdb=" C ALA A 89 " ideal model delta sigma weight residual 1.524 1.485 0.040 1.48e-02 4.57e+03 7.14e+00 ... (remaining 16767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 21868 1.65 - 3.29: 1460 3.29 - 4.94: 262 4.94 - 6.59: 140 6.59 - 8.23: 35 Bond angle restraints: 23765 Sorted by residual: angle pdb=" N ALA D 89 " pdb=" CA ALA D 89 " pdb=" C ALA D 89 " ideal model delta sigma weight residual 112.72 107.01 5.71 1.14e+00 7.69e-01 2.51e+01 angle pdb=" N ALA A 89 " pdb=" CA ALA A 89 " pdb=" C ALA A 89 " ideal model delta sigma weight residual 112.72 107.02 5.70 1.14e+00 7.69e-01 2.50e+01 angle pdb=" N ALA B 89 " pdb=" CA ALA B 89 " pdb=" C ALA B 89 " ideal model delta sigma weight residual 112.72 107.03 5.69 1.14e+00 7.69e-01 2.49e+01 angle pdb=" N ALA E 89 " pdb=" CA ALA E 89 " pdb=" C ALA E 89 " ideal model delta sigma weight residual 112.72 107.03 5.69 1.14e+00 7.69e-01 2.49e+01 angle pdb=" N ALA G 89 " pdb=" CA ALA G 89 " pdb=" C ALA G 89 " ideal model delta sigma weight residual 112.72 107.04 5.68 1.14e+00 7.69e-01 2.49e+01 ... (remaining 23760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 7805 17.06 - 34.12: 532 34.12 - 51.18: 140 51.18 - 68.24: 70 68.24 - 85.30: 70 Dihedral angle restraints: 8617 sinusoidal: 3472 harmonic: 5145 Sorted by residual: dihedral pdb=" CA PRO E 29 " pdb=" C PRO E 29 " pdb=" N PRO E 30 " pdb=" CA PRO E 30 " ideal model delta harmonic sigma weight residual 180.00 149.12 30.88 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA PRO D 29 " pdb=" C PRO D 29 " pdb=" N PRO D 30 " pdb=" CA PRO D 30 " ideal model delta harmonic sigma weight residual 180.00 149.14 30.86 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA PRO F 29 " pdb=" C PRO F 29 " pdb=" N PRO F 30 " pdb=" CA PRO F 30 " ideal model delta harmonic sigma weight residual 180.00 149.14 30.86 0 5.00e+00 4.00e-02 3.81e+01 ... (remaining 8614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1530 0.053 - 0.106: 503 0.106 - 0.159: 83 0.159 - 0.211: 5 0.211 - 0.264: 7 Chirality restraints: 2128 Sorted by residual: chirality pdb=" CA LEU F 88 " pdb=" N LEU F 88 " pdb=" C LEU F 88 " pdb=" CB LEU F 88 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA LEU B 88 " pdb=" N LEU B 88 " pdb=" C LEU B 88 " pdb=" CB LEU B 88 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA LEU E 88 " pdb=" N LEU E 88 " pdb=" C LEU E 88 " pdb=" CB LEU E 88 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 2125 not shown) Planarity restraints: 2912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 87 " -0.026 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C THR C 87 " 0.094 2.00e-02 2.50e+03 pdb=" O THR C 87 " -0.037 2.00e-02 2.50e+03 pdb=" N LEU C 88 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 87 " 0.026 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C THR D 87 " -0.094 2.00e-02 2.50e+03 pdb=" O THR D 87 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU D 88 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 87 " 0.026 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C THR F 87 " -0.094 2.00e-02 2.50e+03 pdb=" O THR F 87 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU F 88 " 0.031 2.00e-02 2.50e+03 ... (remaining 2909 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 119 2.33 - 2.97: 8157 2.97 - 3.61: 25220 3.61 - 4.26: 36775 4.26 - 4.90: 57179 Nonbonded interactions: 127450 Sorted by model distance: nonbonded pdb=" CE1 HIS F 207 " pdb="FE HEC F 606 " model vdw 1.684 3.220 nonbonded pdb=" CE1 HIS G 207 " pdb="FE HEC G 606 " model vdw 1.684 3.220 nonbonded pdb=" CE1 HIS B 207 " pdb="FE HEC B 606 " model vdw 1.684 3.220 nonbonded pdb=" CE1 HIS A 207 " pdb="FE HEC A 606 " model vdw 1.684 3.220 nonbonded pdb=" CE1 HIS E 207 " pdb="FE HEC E 606 " model vdw 1.684 3.220 ... (remaining 127445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.12 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: 2.750 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 29.100 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.550 ------------------------------------------------------------------------------- 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 : 1.768 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: 0.3010 time to fit residues: 177.2305 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 : 1.438 ------------------------------------------------------------------------------- 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 = 55)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.071220 restraints weight = 45192.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.074318 restraints weight = 25621.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.076505 restraints weight = 16834.735| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- 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 : 1.452 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: 0.7708 (mt) cc_final: 0.7502 (mt) REVERT: B 60 LEU cc_start: 0.9145 (mm) cc_final: 0.8889 (pp) REVERT: B 63 GLN cc_start: 0.8809 (mt0) cc_final: 0.8433 (mt0) REVERT: B 79 ASN cc_start: 0.8004 (t0) cc_final: 0.7584 (t0) REVERT: B 95 MET cc_start: 0.8463 (mmm) cc_final: 0.8162 (mmm) REVERT: B 108 PHE cc_start: 0.8881 (p90) cc_final: 0.8678 (p90) REVERT: B 129 LYS cc_start: 0.9338 (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: 0.9010 (tp40) cc_final: 0.8317 (tp40) REVERT: B 204 ASP cc_start: 0.8955 (m-30) cc_final: 0.8559 (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: 0.7747 (m100) REVERT: B 269 ASN cc_start: 0.8105 (m-40) cc_final: 0.7378 (t0) REVERT: B 273 GLN cc_start: 0.8545 (mt0) cc_final: 0.8302 (mt0) REVERT: C 51 LEU cc_start: 0.7600 (mt) cc_final: 0.7382 (mt) REVERT: C 79 ASN cc_start: 0.7864 (t0) cc_final: 0.7583 (t0) REVERT: C 90 THR cc_start: 0.8464 (p) cc_final: 0.8200 (t) REVERT: C 95 MET cc_start: 0.8617 (mmm) cc_final: 0.8213 (mmm) REVERT: C 108 PHE cc_start: 0.8925 (p90) cc_final: 0.8460 (p90) REVERT: C 116 THR cc_start: 0.8900 (m) cc_final: 0.8261 (t) REVERT: C 117 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8037 (mm-40) REVERT: C 139 ILE cc_start: 0.8782 (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: 0.8309 (m-70) cc_final: 0.7636 (m-70) REVERT: C 183 GLN cc_start: 0.4866 (pm20) cc_final: 0.4647 (pm20) REVERT: C 203 GLN cc_start: 0.8950 (tp40) cc_final: 0.8219 (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: 0.8544 (mt) REVERT: C 263 TRP cc_start: 0.8397 (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: 0.7998 (t0) cc_final: 0.7674 (t0) REVERT: D 176 GLN cc_start: 0.7257 (tm-30) cc_final: 0.7005 (tm-30) REVERT: D 203 GLN cc_start: 0.9037 (tp40) cc_final: 0.8377 (tp40) REVERT: D 204 ASP cc_start: 0.8873 (m-30) cc_final: 0.8571 (m-30) REVERT: D 226 ILE cc_start: 0.9026 (tp) cc_final: 0.8817 (tp) REVERT: D 227 ARG cc_start: 0.8826 (mmt180) cc_final: 0.8579 (mtt180) REVERT: D 230 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7719 (mt-10) REVERT: D 242 GLN cc_start: 0.8132 (tp40) cc_final: 0.7838 (tp-100) REVERT: D 269 ASN cc_start: 0.7715 (m-40) cc_final: 0.7156 (t0) REVERT: A 37 ILE cc_start: 0.8635 (pt) cc_final: 0.8284 (pt) REVERT: A 51 LEU cc_start: 0.7653 (mt) cc_final: 0.7443 (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: 0.8825 (m-30) cc_final: 0.8572 (m-30) REVERT: A 226 ILE cc_start: 0.8981 (tp) cc_final: 0.8633 (tp) REVERT: A 230 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7425 (mt-10) REVERT: A 269 ASN cc_start: 0.7578 (m-40) cc_final: 0.7209 (t0) REVERT: E 60 LEU cc_start: 0.9019 (mm) cc_final: 0.8751 (pp) REVERT: E 61 VAL cc_start: 0.9276 (m) cc_final: 0.9074 (p) REVERT: E 63 GLN cc_start: 0.8822 (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: 0.8865 (t80) cc_final: 0.8597 (t80) REVERT: E 146 HIS cc_start: 0.7951 (p-80) cc_final: 0.7629 (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: 0.7987 (tm-30) REVERT: E 242 GLN cc_start: 0.7987 (tp40) cc_final: 0.7504 (tp-100) REVERT: E 266 ILE cc_start: 0.8652 (mp) cc_final: 0.8364 (mp) REVERT: E 269 ASN cc_start: 0.7981 (m-40) cc_final: 0.7033 (m-40) REVERT: E 273 GLN cc_start: 0.8675 (mt0) cc_final: 0.8393 (mt0) REVERT: F 79 ASN cc_start: 0.7976 (t0) cc_final: 0.7651 (t0) REVERT: F 95 MET cc_start: 0.8605 (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: 0.7672 (tm-30) cc_final: 0.7277 (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: 0.8509 (m-30) REVERT: F 226 ILE cc_start: 0.9028 (tp) cc_final: 0.8763 (tp) REVERT: F 227 ARG cc_start: 0.8854 (mmt180) cc_final: 0.8475 (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: 0.7712 (m-40) cc_final: 0.7298 (t0) REVERT: G 46 THR cc_start: 0.8001 (t) cc_final: 0.7533 (p) REVERT: G 79 ASN cc_start: 0.7870 (t0) cc_final: 0.7594 (t0) REVERT: G 108 PHE cc_start: 0.9133 (p90) cc_final: 0.8742 (p90) REVERT: G 140 ASP cc_start: 0.8347 (m-30) cc_final: 0.7924 (t0) REVERT: G 141 ASN cc_start: 0.8803 (t0) cc_final: 0.8418 (t0) REVERT: G 179 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7373 (mt-10) REVERT: G 182 HIS cc_start: 0.8394 (m-70) cc_final: 0.7721 (m170) REVERT: G 183 GLN cc_start: 0.4797 (pm20) cc_final: 0.4568 (pm20) REVERT: G 204 ASP cc_start: 0.8978 (m-30) cc_final: 0.8584 (m-30) REVERT: G 216 LEU cc_start: 0.8745 (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: 0.8181 (mtt180) REVERT: G 230 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7784 (mt-10) REVERT: G 238 LEU cc_start: 0.8927 (mt) cc_final: 0.8657 (mt) REVERT: G 241 ILE cc_start: 0.8874 (pt) cc_final: 0.8570 (pt) REVERT: G 242 GLN cc_start: 0.7874 (tp40) cc_final: 0.7510 (tp-100) REVERT: G 260 ASP cc_start: 0.8010 (t0) cc_final: 0.7762 (t0) REVERT: G 261 LEU cc_start: 0.8102 (pt) cc_final: 0.7756 (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: 0.2977 time to fit residues: 185.4879 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 : 1.433 ------------------------------------------------------------------------------- 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: 0.9980 chunk 105 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 139 optimal weight: 0.2980 chunk 152 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3355 r_free = 0.3355 target = 0.082925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.067832 restraints weight = 45944.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.070669 restraints weight = 26911.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.072702 restraints weight = 18120.974| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.539 16952 Z= 0.263 Angle : 0.954 10.897 23765 Z= 0.361 Chirality : 0.050 0.155 2128 Planarity : 0.005 0.058 2912 Dihedral : 18.117 89.243 2303 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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: -2.47 (0.19), residues: 1792 helix: -1.57 (0.27), 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 D 279 HIS 0.009 0.001 HIS G 276 PHE 0.017 0.002 PHE F 34 TYR 0.015 0.002 TYR B 151 ARG 0.004 0.001 ARG E 197 Details of bonding type rmsd hydrogen bonds : bond 0.03171 ( 154) hydrogen bonds : angle 6.62812 ( 441) covalent geometry : bond 0.00742 (16772) covalent geometry : angle 0.95419 (23765) Misc. bond : bond 0.18200 ( 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 454 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 1.512 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: 0.7794 (m-70) cc_final: 0.7440 (m-70) REVERT: B 60 LEU cc_start: 0.9196 (mm) cc_final: 0.8944 (mm) REVERT: B 62 GLN cc_start: 0.8689 (mm110) cc_final: 0.8074 (mp10) REVERT: B 63 GLN cc_start: 0.8807 (mt0) cc_final: 0.8401 (mt0) REVERT: B 95 MET cc_start: 0.8407 (mmm) cc_final: 0.8136 (mmm) REVERT: B 117 GLN cc_start: 0.8742 (tp-100) cc_final: 0.8503 (tp40) REVERT: B 129 LYS cc_start: 0.9320 (ptpp) cc_final: 0.9029 (mttp) REVERT: B 146 HIS cc_start: 0.8211 (p90) cc_final: 0.7740 (p90) REVERT: B 148 ILE cc_start: 0.9323 (mm) cc_final: 0.9078 (mm) REVERT: B 183 GLN cc_start: 0.7114 (pm20) cc_final: 0.6881 (pm20) REVERT: B 204 ASP cc_start: 0.8941 (m-30) cc_final: 0.8536 (m-30) REVERT: C 46 THR cc_start: 0.8142 (t) cc_final: 0.7663 (p) REVERT: C 51 LEU cc_start: 0.7545 (mt) cc_final: 0.7304 (mt) REVERT: C 79 ASN cc_start: 0.7974 (t0) cc_final: 0.7659 (t0) REVERT: C 90 THR cc_start: 0.8486 (p) cc_final: 0.8244 (t) REVERT: C 95 MET cc_start: 0.8413 (mmm) cc_final: 0.7625 (mmp) REVERT: C 108 PHE cc_start: 0.8930 (p90) cc_final: 0.8540 (p90) REVERT: C 116 THR cc_start: 0.8869 (m) cc_final: 0.8174 (t) REVERT: C 117 GLN cc_start: 0.8340 (mm-40) cc_final: 0.7993 (mm-40) REVERT: C 141 ASN cc_start: 0.8743 (t0) cc_final: 0.8424 (t0) REVERT: C 179 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7687 (mt-10) REVERT: C 182 HIS cc_start: 0.8391 (m-70) cc_final: 0.7595 (m-70) REVERT: C 183 GLN cc_start: 0.6561 (pm20) cc_final: 0.6061 (pm20) REVERT: C 203 GLN cc_start: 0.9033 (tp40) cc_final: 0.8161 (tp40) REVERT: C 204 ASP cc_start: 0.8823 (m-30) cc_final: 0.8563 (m-30) REVERT: C 230 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7759 (mt-10) REVERT: C 238 LEU cc_start: 0.8902 (mp) cc_final: 0.8678 (mt) REVERT: C 260 ASP cc_start: 0.8064 (t0) cc_final: 0.7822 (t0) REVERT: C 261 LEU cc_start: 0.8182 (pt) cc_final: 0.7907 (pt) REVERT: C 269 ASN cc_start: 0.7453 (m-40) cc_final: 0.6879 (m-40) REVERT: C 279 TRP cc_start: 0.7830 (t-100) cc_final: 0.7573 (t-100) REVERT: D 51 LEU cc_start: 0.7634 (mt) cc_final: 0.7388 (mt) REVERT: D 54 HIS cc_start: 0.7540 (m-70) cc_final: 0.7327 (m-70) REVERT: D 197 ARG cc_start: 0.6677 (ttt180) cc_final: 0.6432 (ttt180) REVERT: D 203 GLN cc_start: 0.9052 (tp40) cc_final: 0.8434 (tp40) REVERT: D 204 ASP cc_start: 0.8900 (m-30) cc_final: 0.8583 (m-30) REVERT: D 226 ILE cc_start: 0.9127 (tp) cc_final: 0.8892 (tp) REVERT: D 227 ARG cc_start: 0.8587 (mmt90) cc_final: 0.8343 (mmt90) REVERT: D 230 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7696 (mt-10) REVERT: D 238 LEU cc_start: 0.8931 (mt) cc_final: 0.8725 (mt) REVERT: D 242 GLN cc_start: 0.8250 (tp40) cc_final: 0.7819 (tp-100) REVERT: D 269 ASN cc_start: 0.7924 (m-40) cc_final: 0.7533 (m-40) REVERT: A 34 PHE cc_start: 0.8774 (p90) cc_final: 0.8519 (p90) REVERT: A 37 ILE cc_start: 0.8492 (pt) cc_final: 0.8141 (pt) REVERT: A 90 THR cc_start: 0.8525 (p) cc_final: 0.8295 (t) REVERT: A 135 HIS cc_start: 0.7687 (p-80) cc_final: 0.7370 (p-80) REVERT: A 141 ASN cc_start: 0.8706 (t0) cc_final: 0.8392 (t0) REVERT: A 144 ASP cc_start: 0.7876 (p0) cc_final: 0.7431 (p0) REVERT: A 176 GLN cc_start: 0.7747 (tm-30) cc_final: 0.7173 (tm-30) REVERT: A 203 GLN cc_start: 0.8955 (tp40) cc_final: 0.8567 (tp40) REVERT: A 204 ASP cc_start: 0.8859 (m-30) cc_final: 0.8606 (m-30) REVERT: A 227 ARG cc_start: 0.8873 (mtt180) cc_final: 0.8473 (mtt180) REVERT: A 230 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7533 (mt-10) REVERT: A 269 ASN cc_start: 0.7702 (m-40) cc_final: 0.7285 (m-40) REVERT: E 51 LEU cc_start: 0.7939 (mt) cc_final: 0.7700 (mt) REVERT: E 54 HIS cc_start: 0.7584 (m-70) cc_final: 0.7364 (m-70) REVERT: E 63 GLN cc_start: 0.8797 (mt0) cc_final: 0.8474 (mt0) REVERT: E 79 ASN cc_start: 0.8156 (t0) cc_final: 0.7846 (t0) REVERT: E 133 TYR cc_start: 0.8829 (t80) cc_final: 0.8509 (t80) REVERT: E 203 GLN cc_start: 0.8997 (tp40) cc_final: 0.8506 (tp40) REVERT: E 204 ASP cc_start: 0.8697 (m-30) cc_final: 0.8414 (m-30) REVERT: E 216 LEU cc_start: 0.9120 (tt) cc_final: 0.8900 (tt) REVERT: E 242 GLN cc_start: 0.8040 (tp40) cc_final: 0.7657 (tp-100) REVERT: F 51 LEU cc_start: 0.7631 (mt) cc_final: 0.7400 (mt) REVERT: F 62 GLN cc_start: 0.8789 (mm110) cc_final: 0.8583 (mm110) REVERT: F 79 ASN cc_start: 0.7854 (t0) cc_final: 0.7511 (t0) REVERT: F 95 MET cc_start: 0.8430 (mmm) cc_final: 0.8210 (mmp) REVERT: F 105 PHE cc_start: 0.8350 (m-80) cc_final: 0.8135 (m-80) REVERT: F 203 GLN cc_start: 0.9012 (tp40) cc_final: 0.8592 (tp40) REVERT: F 204 ASP cc_start: 0.8962 (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: 0.8533 (mmt90) cc_final: 0.8228 (mmt90) REVERT: F 230 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7601 (mt-10) REVERT: F 243 LYS cc_start: 0.8862 (tmtt) cc_final: 0.8603 (tptp) REVERT: F 255 LYS cc_start: 0.8779 (pttm) cc_final: 0.8503 (ptpp) REVERT: F 263 TRP cc_start: 0.8589 (m100) cc_final: 0.8202 (m100) REVERT: F 269 ASN cc_start: 0.7740 (m-40) cc_final: 0.7065 (m-40) REVERT: F 279 TRP cc_start: 0.7858 (t-100) cc_final: 0.7608 (t60) REVERT: G 37 ILE cc_start: 0.8510 (pt) cc_final: 0.7871 (mt) REVERT: G 46 THR cc_start: 0.8324 (t) cc_final: 0.7861 (p) REVERT: G 79 ASN cc_start: 0.8069 (t0) cc_final: 0.7744 (t0) REVERT: G 117 GLN cc_start: 0.8382 (mm110) cc_final: 0.8122 (mm110) REVERT: G 135 HIS cc_start: 0.7230 (p90) cc_final: 0.6939 (p-80) REVERT: G 141 ASN cc_start: 0.8684 (t0) cc_final: 0.8467 (t0) REVERT: G 179 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7494 (mt-10) REVERT: G 182 HIS cc_start: 0.8453 (m-70) cc_final: 0.7463 (m170) REVERT: G 183 GLN cc_start: 0.6623 (pm20) cc_final: 0.6148 (pm20) REVERT: G 204 ASP cc_start: 0.8993 (m-30) cc_final: 0.8569 (m-30) REVERT: G 226 ILE cc_start: 0.8955 (tp) cc_final: 0.8665 (tp) REVERT: G 227 ARG cc_start: 0.8390 (mmt90) cc_final: 0.8160 (mmt90) REVERT: G 230 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7732 (mt-10) REVERT: G 238 LEU cc_start: 0.8852 (mt) cc_final: 0.8417 (mp) REVERT: G 241 ILE cc_start: 0.9020 (pt) cc_final: 0.8501 (pt) REVERT: G 242 GLN cc_start: 0.7942 (tp40) cc_final: 0.7516 (tp-100) REVERT: G 244 ASP cc_start: 0.7977 (t0) cc_final: 0.7737 (t0) REVERT: G 260 ASP cc_start: 0.8107 (t0) cc_final: 0.7834 (t0) REVERT: G 261 LEU cc_start: 0.8191 (pt) cc_final: 0.7835 (pt) REVERT: G 263 TRP cc_start: 0.8419 (m100) cc_final: 0.7915 (m100) REVERT: G 269 ASN cc_start: 0.7642 (m-40) cc_final: 0.7036 (m-40) outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.2920 time to fit residues: 189.9383 Evaluate side-chains 404 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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: 0.2980 chunk 170 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 118 optimal weight: 0.2980 chunk 2 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 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 E 273 GLN 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 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 = 0.3397 r_free = 0.3397 target = 0.085263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.069675 restraints weight = 45656.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.072749 restraints weight = 25890.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.074890 restraints weight = 17029.153| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.453 16952 Z= 0.187 Angle : 0.863 9.892 23765 Z= 0.332 Chirality : 0.047 0.144 2128 Planarity : 0.005 0.049 2912 Dihedral : 18.093 89.933 2303 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.39 % Favored : 86.61 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % 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: -2.10 (0.20), residues: 1792 helix: -1.76 (0.27), residues: 280 sheet: -0.98 (0.57), residues: 70 loop : -1.45 (0.17), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 279 HIS 0.009 0.001 HIS E 146 PHE 0.016 0.002 PHE E 103 TYR 0.014 0.002 TYR E 38 ARG 0.003 0.000 ARG E 197 Details of bonding type rmsd hydrogen bonds : bond 0.02786 ( 154) hydrogen bonds : angle 6.40747 ( 441) covalent geometry : bond 0.00522 (16772) covalent geometry : angle 0.86273 (23765) Misc. bond : bond 0.13675 ( 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 462 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 462 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 LEU cc_start: 0.7567 (mt) cc_final: 0.7365 (mt) REVERT: B 54 HIS cc_start: 0.7540 (m-70) cc_final: 0.7197 (m-70) REVERT: B 63 GLN cc_start: 0.8926 (mt0) cc_final: 0.8448 (mt0) REVERT: B 95 MET cc_start: 0.8765 (mmm) cc_final: 0.8449 (mmp) REVERT: B 129 LYS cc_start: 0.9258 (ptpp) cc_final: 0.9025 (mttp) REVERT: B 146 HIS cc_start: 0.8206 (p90) cc_final: 0.7758 (p90) REVERT: B 148 ILE cc_start: 0.9236 (mm) cc_final: 0.8953 (mm) REVERT: B 200 PHE cc_start: 0.8245 (m-80) cc_final: 0.7602 (m-80) REVERT: B 203 GLN cc_start: 0.9037 (tp40) cc_final: 0.8144 (tp40) REVERT: B 204 ASP cc_start: 0.8810 (m-30) cc_final: 0.7836 (t0) REVERT: C 46 THR cc_start: 0.8170 (t) cc_final: 0.7652 (p) REVERT: C 79 ASN cc_start: 0.7917 (t0) cc_final: 0.7625 (t0) REVERT: C 90 THR cc_start: 0.8518 (p) cc_final: 0.8271 (t) REVERT: C 95 MET cc_start: 0.8533 (mmm) cc_final: 0.8130 (mmm) REVERT: C 108 PHE cc_start: 0.8970 (p90) cc_final: 0.8176 (p90) REVERT: C 135 HIS cc_start: 0.7342 (p90) cc_final: 0.7027 (p-80) REVERT: C 179 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7459 (mt-10) REVERT: C 182 HIS cc_start: 0.8245 (m-70) cc_final: 0.7430 (m-70) REVERT: C 183 GLN cc_start: 0.6219 (pm20) cc_final: 0.5881 (pm20) REVERT: C 203 GLN cc_start: 0.9014 (tp40) cc_final: 0.8149 (tp40) REVERT: C 204 ASP cc_start: 0.8780 (m-30) cc_final: 0.8498 (m-30) REVERT: C 238 LEU cc_start: 0.8966 (mp) cc_final: 0.8707 (mt) REVERT: C 269 ASN cc_start: 0.7415 (m-40) cc_final: 0.6708 (m-40) REVERT: C 279 TRP cc_start: 0.7771 (t-100) cc_final: 0.7385 (t-100) REVERT: D 51 LEU cc_start: 0.7552 (mt) cc_final: 0.7329 (mt) REVERT: D 79 ASN cc_start: 0.7927 (t0) cc_final: 0.7628 (t0) REVERT: D 108 PHE cc_start: 0.8834 (p90) cc_final: 0.8630 (p90) REVERT: D 179 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7301 (mt-10) REVERT: D 203 GLN cc_start: 0.9018 (tp40) cc_final: 0.8357 (tp40) REVERT: D 204 ASP cc_start: 0.8878 (m-30) cc_final: 0.8535 (m-30) REVERT: D 226 ILE cc_start: 0.9087 (tp) cc_final: 0.8806 (tp) REVERT: D 230 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7612 (mt-10) REVERT: D 238 LEU cc_start: 0.8974 (mt) cc_final: 0.8766 (mt) REVERT: D 242 GLN cc_start: 0.8249 (tp40) cc_final: 0.7822 (tp-100) REVERT: D 269 ASN cc_start: 0.7818 (m-40) cc_final: 0.7318 (m-40) REVERT: A 37 ILE cc_start: 0.8469 (pt) cc_final: 0.8078 (pt) REVERT: A 129 LYS cc_start: 0.9228 (ptpp) cc_final: 0.8970 (mttm) REVERT: A 135 HIS cc_start: 0.7759 (p-80) cc_final: 0.7147 (p-80) REVERT: A 176 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7484 (tm-30) REVERT: A 203 GLN cc_start: 0.8942 (tp40) cc_final: 0.8510 (tp40) REVERT: A 204 ASP cc_start: 0.8877 (m-30) cc_final: 0.8602 (m-30) REVERT: A 227 ARG cc_start: 0.8772 (mtt180) cc_final: 0.8361 (mtt180) REVERT: A 230 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7337 (mt-10) REVERT: A 260 ASP cc_start: 0.7926 (t0) cc_final: 0.7583 (t0) REVERT: A 261 LEU cc_start: 0.8269 (pt) cc_final: 0.7854 (pt) REVERT: A 269 ASN cc_start: 0.7694 (m-40) cc_final: 0.7084 (m-40) REVERT: E 51 LEU cc_start: 0.7755 (mt) cc_final: 0.7536 (mt) REVERT: E 54 HIS cc_start: 0.7437 (m-70) cc_final: 0.7080 (m-70) REVERT: E 63 GLN cc_start: 0.8797 (mt0) cc_final: 0.8423 (mt0) REVERT: E 79 ASN cc_start: 0.8116 (t0) cc_final: 0.7739 (t0) REVERT: E 133 TYR cc_start: 0.8849 (t80) cc_final: 0.8484 (t80) REVERT: E 135 HIS cc_start: 0.7871 (p-80) cc_final: 0.7615 (p-80) REVERT: E 176 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7281 (tm-30) REVERT: E 203 GLN cc_start: 0.8955 (tp40) cc_final: 0.8354 (tp40) REVERT: E 204 ASP cc_start: 0.8691 (m-30) cc_final: 0.8360 (m-30) REVERT: E 213 ASP cc_start: 0.8519 (t0) cc_final: 0.8316 (t0) REVERT: E 216 LEU cc_start: 0.9083 (tt) cc_final: 0.8820 (tt) REVERT: E 228 GLN cc_start: 0.8348 (tt0) cc_final: 0.7905 (tm-30) REVERT: E 230 GLU cc_start: 0.8567 (tt0) cc_final: 0.8078 (tt0) REVERT: E 238 LEU cc_start: 0.8996 (mp) cc_final: 0.8785 (mp) REVERT: E 269 ASN cc_start: 0.7964 (m-40) cc_final: 0.7289 (m-40) REVERT: F 51 LEU cc_start: 0.7623 (mt) cc_final: 0.7411 (mt) REVERT: F 79 ASN cc_start: 0.7789 (t0) cc_final: 0.7467 (t0) REVERT: F 95 MET cc_start: 0.8282 (mmm) cc_final: 0.7831 (mmm) REVERT: F 129 LYS cc_start: 0.9159 (mttp) cc_final: 0.8925 (tppt) REVERT: F 135 HIS cc_start: 0.7593 (p90) cc_final: 0.7010 (p90) REVERT: F 203 GLN cc_start: 0.8966 (tp40) cc_final: 0.8527 (tp40) REVERT: F 204 ASP cc_start: 0.8925 (m-30) cc_final: 0.8542 (m-30) REVERT: F 226 ILE cc_start: 0.9028 (tp) cc_final: 0.8765 (tp) REVERT: F 227 ARG cc_start: 0.8431 (mmt90) cc_final: 0.8188 (mmt90) REVERT: F 230 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7639 (mt-10) REVERT: F 243 LYS cc_start: 0.8778 (tmtt) cc_final: 0.8498 (tptp) REVERT: F 255 LYS cc_start: 0.8794 (pttm) cc_final: 0.8498 (ptpp) REVERT: F 263 TRP cc_start: 0.8499 (m100) cc_final: 0.8033 (m100) REVERT: F 269 ASN cc_start: 0.8155 (m-40) cc_final: 0.7178 (m-40) REVERT: G 46 THR cc_start: 0.8345 (t) cc_final: 0.7857 (p) REVERT: G 79 ASN cc_start: 0.8050 (t0) cc_final: 0.7687 (t0) REVERT: G 108 PHE cc_start: 0.9046 (p90) cc_final: 0.8432 (p90) REVERT: G 116 THR cc_start: 0.8860 (t) cc_final: 0.8441 (t) REVERT: G 117 GLN cc_start: 0.8356 (mm110) cc_final: 0.8092 (mm110) REVERT: G 179 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7439 (mt-10) REVERT: G 182 HIS cc_start: 0.8090 (m-70) cc_final: 0.7180 (m170) REVERT: G 183 GLN cc_start: 0.6016 (pm20) cc_final: 0.5696 (pm20) REVERT: G 203 GLN cc_start: 0.9104 (tp40) cc_final: 0.8148 (tp40) REVERT: G 204 ASP cc_start: 0.8898 (m-30) cc_final: 0.8486 (m-30) REVERT: G 226 ILE cc_start: 0.8888 (tp) cc_final: 0.8591 (tp) REVERT: G 227 ARG cc_start: 0.8325 (mmt90) cc_final: 0.7939 (mmt90) REVERT: G 230 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7574 (mt-10) REVERT: G 241 ILE cc_start: 0.8957 (pt) cc_final: 0.8383 (pt) REVERT: G 242 GLN cc_start: 0.7970 (tp40) cc_final: 0.7497 (tp-100) REVERT: G 244 ASP cc_start: 0.7977 (t0) cc_final: 0.7671 (t0) REVERT: G 260 ASP cc_start: 0.8111 (t0) cc_final: 0.7773 (t0) REVERT: G 261 LEU cc_start: 0.7991 (pt) cc_final: 0.7645 (pt) REVERT: G 263 TRP cc_start: 0.8277 (m100) cc_final: 0.7906 (m100) REVERT: G 266 ILE cc_start: 0.8622 (mp) cc_final: 0.8364 (mp) REVERT: G 269 ASN cc_start: 0.7530 (m-40) cc_final: 0.6990 (m-40) outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.2933 time to fit residues: 195.5782 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 : 1.630 ------------------------------------------------------------------------------- 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: 0.7980 chunk 34 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 73 optimal weight: 0.0050 chunk 143 optimal weight: 2.9990 chunk 63 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN C 63 GLN C 228 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 135 HIS D 146 HIS D 228 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN A 228 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN E 228 GLN F 63 GLN F 228 GLN ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 273 GLN G 63 GLN G 228 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.085886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.070478 restraints weight = 46269.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.073548 restraints weight = 26143.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.075684 restraints weight = 17116.072| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.430 16952 Z= 0.175 Angle : 0.848 9.869 23765 Z= 0.325 Chirality : 0.047 0.144 2128 Planarity : 0.005 0.043 2912 Dihedral : 18.005 89.930 2303 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.04 % 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: -2.09 (0.20), residues: 1792 helix: -1.75 (0.27), residues: 287 sheet: -1.36 (0.57), residues: 70 loop : -1.42 (0.18), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 270 HIS 0.005 0.001 HIS G 239 PHE 0.011 0.001 PHE G 34 TYR 0.012 0.002 TYR A 133 ARG 0.003 0.000 ARG E 197 Details of bonding type rmsd hydrogen bonds : bond 0.02684 ( 154) hydrogen bonds : angle 6.27929 ( 441) covalent geometry : bond 0.00482 (16772) covalent geometry : angle 0.84819 (23765) Misc. bond : bond 0.12957 ( 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 447 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 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: symmetry clash revert: symmetry clash REVERT: B 46 THR cc_start: 0.8172 (t) cc_final: 0.7661 (p) REVERT: B 51 LEU cc_start: 0.7485 (mt) cc_final: 0.7283 (mt) REVERT: B 60 LEU cc_start: 0.9144 (mm) cc_final: 0.8861 (mm) REVERT: B 63 GLN cc_start: 0.8731 (mt0) cc_final: 0.8279 (mt0) REVERT: B 95 MET cc_start: 0.8749 (mmm) cc_final: 0.8341 (mmp) REVERT: B 135 HIS cc_start: 0.7530 (p90) cc_final: 0.7273 (p-80) REVERT: B 146 HIS cc_start: 0.8221 (p90) cc_final: 0.7804 (p90) REVERT: B 148 ILE cc_start: 0.9212 (mm) cc_final: 0.8924 (mm) REVERT: B 203 GLN cc_start: 0.9040 (tp40) cc_final: 0.8108 (tp40) REVERT: B 204 ASP cc_start: 0.8768 (m-30) cc_final: 0.7773 (t0) REVERT: B 277 TRP cc_start: 0.8512 (t-100) cc_final: 0.8152 (t-100) REVERT: C 46 THR cc_start: 0.8154 (t) cc_final: 0.7628 (p) REVERT: C 79 ASN cc_start: 0.7909 (t0) cc_final: 0.7621 (t0) REVERT: C 90 THR cc_start: 0.8538 (p) cc_final: 0.8256 (t) REVERT: C 129 LYS cc_start: 0.9227 (mttp) cc_final: 0.8993 (tppt) REVERT: C 135 HIS cc_start: 0.7285 (p90) cc_final: 0.7015 (p-80) REVERT: C 139 ILE cc_start: 0.8725 (tp) cc_final: 0.8513 (tp) REVERT: C 179 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7496 (mt-10) REVERT: C 182 HIS cc_start: 0.8278 (m-70) cc_final: 0.7391 (m170) REVERT: C 203 GLN cc_start: 0.9014 (tp40) cc_final: 0.8136 (tp40) REVERT: C 204 ASP cc_start: 0.8736 (m-30) cc_final: 0.8406 (m-30) REVERT: C 227 ARG cc_start: 0.8634 (mtt180) cc_final: 0.8004 (mtt180) REVERT: C 230 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7635 (mt-10) REVERT: C 238 LEU cc_start: 0.8977 (mp) cc_final: 0.8745 (mt) REVERT: C 269 ASN cc_start: 0.7293 (m-40) cc_final: 0.6673 (m-40) REVERT: C 279 TRP cc_start: 0.7768 (t-100) cc_final: 0.7493 (t-100) REVERT: D 79 ASN cc_start: 0.7896 (t0) cc_final: 0.7587 (t0) REVERT: D 133 TYR cc_start: 0.8734 (t80) cc_final: 0.8527 (t80) REVERT: D 135 HIS cc_start: 0.7490 (p90) cc_final: 0.7153 (p-80) REVERT: D 179 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7500 (mt-10) REVERT: D 203 GLN cc_start: 0.9017 (tp40) cc_final: 0.8401 (tp40) REVERT: D 204 ASP cc_start: 0.8852 (m-30) cc_final: 0.8533 (m-30) REVERT: D 213 ASP cc_start: 0.8633 (t0) cc_final: 0.8349 (t0) REVERT: D 226 ILE cc_start: 0.9053 (tp) cc_final: 0.8802 (tp) REVERT: D 230 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7636 (mt-10) REVERT: D 242 GLN cc_start: 0.8230 (tp40) cc_final: 0.7949 (tp40) REVERT: D 260 ASP cc_start: 0.8028 (t0) cc_final: 0.7780 (t0) REVERT: D 261 LEU cc_start: 0.8366 (pt) cc_final: 0.8004 (pt) REVERT: D 269 ASN cc_start: 0.7714 (m-40) cc_final: 0.7242 (m-40) REVERT: A 46 THR cc_start: 0.8263 (t) cc_final: 0.7759 (p) REVERT: A 129 LYS cc_start: 0.9253 (ptpp) cc_final: 0.9034 (mttm) REVERT: A 135 HIS cc_start: 0.7831 (p-80) cc_final: 0.7385 (p-80) REVERT: A 176 GLN cc_start: 0.7659 (tm-30) cc_final: 0.7354 (tm-30) REVERT: A 203 GLN cc_start: 0.8733 (tp40) cc_final: 0.8310 (tp40) REVERT: A 204 ASP cc_start: 0.8842 (m-30) cc_final: 0.8551 (m-30) REVERT: A 213 ASP cc_start: 0.8485 (t0) cc_final: 0.8270 (t0) REVERT: A 227 ARG cc_start: 0.8693 (mtt180) cc_final: 0.8311 (mtt180) REVERT: A 230 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7198 (mt-10) REVERT: A 260 ASP cc_start: 0.7917 (t0) cc_final: 0.7554 (t0) REVERT: A 261 LEU cc_start: 0.8231 (pt) cc_final: 0.7816 (pt) REVERT: A 269 ASN cc_start: 0.7577 (m-40) cc_final: 0.7124 (m-40) REVERT: E 51 LEU cc_start: 0.7680 (mt) cc_final: 0.7458 (mt) REVERT: E 63 GLN cc_start: 0.8768 (mt0) cc_final: 0.8400 (mt0) REVERT: E 79 ASN cc_start: 0.8128 (t0) cc_final: 0.7576 (t0) REVERT: E 133 TYR cc_start: 0.8792 (t80) cc_final: 0.8421 (t80) REVERT: E 135 HIS cc_start: 0.7934 (p-80) cc_final: 0.7566 (p-80) REVERT: E 176 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7419 (tm-30) REVERT: E 203 GLN cc_start: 0.8972 (tp40) cc_final: 0.8397 (tp40) REVERT: E 204 ASP cc_start: 0.8717 (m-30) cc_final: 0.8412 (m-30) REVERT: E 230 GLU cc_start: 0.8522 (tt0) cc_final: 0.8045 (tt0) REVERT: E 269 ASN cc_start: 0.7797 (m-40) cc_final: 0.7243 (m-40) REVERT: F 51 LEU cc_start: 0.7506 (mt) cc_final: 0.7271 (mt) REVERT: F 79 ASN cc_start: 0.7786 (t0) cc_final: 0.7454 (t0) REVERT: F 95 MET cc_start: 0.8584 (mmm) cc_final: 0.8290 (mmm) REVERT: F 109 ARG cc_start: 0.8911 (mmm-85) cc_final: 0.8441 (tpp-160) REVERT: F 129 LYS cc_start: 0.9147 (mttp) cc_final: 0.8904 (tppt) REVERT: F 130 ASP cc_start: 0.8089 (t0) cc_final: 0.7850 (t0) REVERT: F 176 GLN cc_start: 0.7486 (tm-30) cc_final: 0.7216 (tm-30) REVERT: F 203 GLN cc_start: 0.8989 (tp40) cc_final: 0.8203 (tp40) REVERT: F 204 ASP cc_start: 0.8877 (m-30) cc_final: 0.8443 (m-30) REVERT: F 226 ILE cc_start: 0.9031 (tp) cc_final: 0.8743 (tp) REVERT: F 227 ARG cc_start: 0.8496 (mmt90) cc_final: 0.8218 (mmt90) REVERT: F 230 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7565 (mt-10) REVERT: F 243 LYS cc_start: 0.8776 (tmtt) cc_final: 0.8514 (tptp) REVERT: F 263 TRP cc_start: 0.8463 (m100) cc_final: 0.7972 (m100) REVERT: F 269 ASN cc_start: 0.7727 (m-40) cc_final: 0.7052 (m-40) REVERT: G 46 THR cc_start: 0.8343 (t) cc_final: 0.7840 (p) REVERT: G 79 ASN cc_start: 0.8079 (t0) cc_final: 0.7687 (t0) REVERT: G 116 THR cc_start: 0.8841 (t) cc_final: 0.8423 (t) REVERT: G 117 GLN cc_start: 0.8338 (mm110) cc_final: 0.8060 (mm110) REVERT: G 179 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7432 (mt-10) REVERT: G 182 HIS cc_start: 0.8082 (m-70) cc_final: 0.7184 (m170) REVERT: G 203 GLN cc_start: 0.9121 (tp40) cc_final: 0.8163 (tp40) REVERT: G 204 ASP cc_start: 0.8876 (m-30) cc_final: 0.8545 (m-30) REVERT: G 241 ILE cc_start: 0.8985 (pt) cc_final: 0.8546 (pt) REVERT: G 242 GLN cc_start: 0.8040 (tp40) cc_final: 0.7611 (tp40) REVERT: G 260 ASP cc_start: 0.8113 (t0) cc_final: 0.7802 (t0) REVERT: G 261 LEU cc_start: 0.7996 (pt) cc_final: 0.7644 (pt) REVERT: G 263 TRP cc_start: 0.8228 (m100) cc_final: 0.7861 (m100) REVERT: G 269 ASN cc_start: 0.7537 (m-40) cc_final: 0.6945 (m-40) outliers start: 0 outliers final: 0 residues processed: 447 average time/residue: 0.2868 time to fit residues: 185.4907 Evaluate side-chains 422 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 1.634 ------------------------------------------------------------------------------- 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: 5.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 94 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 119 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 HIS D 63 GLN D 228 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN A 146 HIS A 228 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 GLN ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN G 135 HIS G 146 HIS G 228 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.086228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.071201 restraints weight = 45883.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.074168 restraints weight = 26446.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.076228 restraints weight = 17498.155| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.451 16952 Z= 0.182 Angle : 0.852 9.856 23765 Z= 0.329 Chirality : 0.047 0.153 2128 Planarity : 0.004 0.040 2912 Dihedral : 18.104 89.397 2303 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.04 % 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: -2.13 (0.20), residues: 1792 helix: -1.85 (0.27), residues: 287 sheet: -1.47 (0.58), residues: 70 loop : -1.43 (0.18), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 279 HIS 0.007 0.001 HIS G 276 PHE 0.017 0.001 PHE D 103 TYR 0.012 0.002 TYR B 151 ARG 0.004 0.000 ARG D 227 Details of bonding type rmsd hydrogen bonds : bond 0.02749 ( 154) hydrogen bonds : angle 6.48484 ( 441) covalent geometry : bond 0.00510 (16772) covalent geometry : angle 0.85206 (23765) Misc. bond : bond 0.12882 ( 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 453 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 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: 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: 0.9154 (mm) cc_final: 0.8879 (mm) REVERT: B 63 GLN cc_start: 0.8778 (mt0) cc_final: 0.8471 (mt0) REVERT: B 95 MET cc_start: 0.8732 (mmm) cc_final: 0.8384 (mmp) REVERT: B 108 PHE cc_start: 0.8933 (p90) cc_final: 0.8558 (p90) REVERT: B 109 ARG cc_start: 0.8936 (mmt180) cc_final: 0.8569 (mmt180) REVERT: B 135 HIS cc_start: 0.7329 (p90) cc_final: 0.7129 (p90) REVERT: B 176 GLN cc_start: 0.7495 (tm-30) cc_final: 0.7205 (tm-30) REVERT: B 203 GLN cc_start: 0.9033 (tp40) cc_final: 0.8305 (tp40) REVERT: B 204 ASP cc_start: 0.8775 (m-30) cc_final: 0.8344 (m-30) REVERT: B 227 ARG cc_start: 0.9160 (mtt180) cc_final: 0.8723 (mtt180) REVERT: B 228 GLN cc_start: 0.8518 (tt0) cc_final: 0.8242 (tm-30) REVERT: B 230 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7631 (mt-10) REVERT: B 255 LYS cc_start: 0.8785 (pttm) cc_final: 0.8578 (ptpp) REVERT: B 277 TRP cc_start: 0.8525 (t-100) cc_final: 0.8198 (t-100) REVERT: C 46 THR cc_start: 0.8252 (t) cc_final: 0.7718 (p) REVERT: C 51 LEU cc_start: 0.7279 (mt) cc_final: 0.7074 (mt) REVERT: C 90 THR cc_start: 0.8543 (p) cc_final: 0.8264 (t) REVERT: C 95 MET cc_start: 0.8651 (mmp) cc_final: 0.8331 (mmp) REVERT: C 108 PHE cc_start: 0.8992 (p90) cc_final: 0.8659 (p90) REVERT: C 135 HIS cc_start: 0.7461 (p90) cc_final: 0.7134 (p90) REVERT: C 139 ILE cc_start: 0.8703 (tp) cc_final: 0.8476 (tp) REVERT: C 179 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7273 (mt-10) REVERT: C 182 HIS cc_start: 0.8315 (m-70) cc_final: 0.7373 (m170) REVERT: C 183 GLN cc_start: 0.6058 (pm20) cc_final: 0.5511 (pm20) REVERT: C 203 GLN cc_start: 0.8793 (tp40) cc_final: 0.7787 (tp40) REVERT: C 204 ASP cc_start: 0.8736 (m-30) cc_final: 0.8400 (m-30) REVERT: C 227 ARG cc_start: 0.8575 (mtt180) cc_final: 0.7997 (mtt180) REVERT: C 230 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7607 (mt-10) REVERT: C 238 LEU cc_start: 0.8956 (mp) cc_final: 0.8553 (mp) REVERT: C 269 ASN cc_start: 0.7404 (m-40) cc_final: 0.6731 (m-40) REVERT: D 46 THR cc_start: 0.8191 (t) cc_final: 0.7796 (t) REVERT: D 79 ASN cc_start: 0.7907 (t0) cc_final: 0.7605 (t0) REVERT: D 108 PHE cc_start: 0.8942 (p90) cc_final: 0.8117 (p90) REVERT: D 179 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7224 (mt-10) REVERT: D 183 GLN cc_start: 0.7209 (pm20) cc_final: 0.6560 (pm20) REVERT: D 203 GLN cc_start: 0.8800 (tp40) cc_final: 0.8182 (tp40) REVERT: D 204 ASP cc_start: 0.8848 (m-30) cc_final: 0.8544 (m-30) REVERT: D 213 ASP cc_start: 0.8710 (t0) cc_final: 0.8405 (t0) REVERT: D 216 LEU cc_start: 0.9111 (tt) cc_final: 0.8904 (tt) REVERT: D 226 ILE cc_start: 0.9068 (tp) cc_final: 0.8838 (tp) REVERT: D 227 ARG cc_start: 0.8656 (mmt180) cc_final: 0.8439 (mtt180) REVERT: D 230 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7534 (mt-10) REVERT: D 242 GLN cc_start: 0.8227 (tp40) cc_final: 0.7940 (tp40) REVERT: D 260 ASP cc_start: 0.8058 (t0) cc_final: 0.7827 (t0) REVERT: D 261 LEU cc_start: 0.8369 (pt) cc_final: 0.8011 (pt) REVERT: D 269 ASN cc_start: 0.7712 (m-40) cc_final: 0.7127 (m-40) REVERT: A 37 ILE cc_start: 0.8514 (pt) cc_final: 0.8229 (pt) REVERT: A 51 LEU cc_start: 0.7646 (mt) cc_final: 0.7427 (mt) REVERT: A 79 ASN cc_start: 0.7712 (t0) cc_final: 0.7348 (t0) REVERT: A 107 ASP cc_start: 0.8320 (t70) cc_final: 0.8090 (t0) REVERT: A 129 LYS cc_start: 0.9250 (ptpp) cc_final: 0.9033 (mttm) REVERT: A 135 HIS cc_start: 0.7829 (p-80) cc_final: 0.7367 (p90) REVERT: A 176 GLN cc_start: 0.7647 (tm-30) cc_final: 0.7310 (tm-30) REVERT: A 203 GLN cc_start: 0.8733 (tp40) cc_final: 0.8257 (tp40) REVERT: A 213 ASP cc_start: 0.8469 (t0) cc_final: 0.8231 (t0) REVERT: A 226 ILE cc_start: 0.9074 (tp) cc_final: 0.8615 (tp) REVERT: A 227 ARG cc_start: 0.8665 (mtt180) cc_final: 0.8330 (mtt180) REVERT: A 228 GLN cc_start: 0.8477 (tt0) cc_final: 0.8263 (tm-30) REVERT: A 230 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7169 (mt-10) REVERT: A 260 ASP cc_start: 0.7979 (t0) cc_final: 0.7608 (t0) REVERT: A 261 LEU cc_start: 0.8295 (pt) cc_final: 0.7899 (pt) REVERT: A 269 ASN cc_start: 0.7706 (m-40) cc_final: 0.7101 (m-40) REVERT: E 51 LEU cc_start: 0.7735 (mt) cc_final: 0.7523 (mt) REVERT: E 60 LEU cc_start: 0.9101 (mm) cc_final: 0.8898 (mm) REVERT: E 63 GLN cc_start: 0.8782 (mt0) cc_final: 0.8415 (mt0) REVERT: E 79 ASN cc_start: 0.8081 (t0) cc_final: 0.7701 (t0) REVERT: E 108 PHE cc_start: 0.8884 (p90) cc_final: 0.8628 (p90) REVERT: E 129 LYS cc_start: 0.9056 (ptpp) cc_final: 0.8833 (mttp) REVERT: E 133 TYR cc_start: 0.8793 (t80) cc_final: 0.8402 (t80) REVERT: E 135 HIS cc_start: 0.8051 (p-80) cc_final: 0.7663 (p-80) REVERT: E 176 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7461 (tm-30) REVERT: E 203 GLN cc_start: 0.8952 (tp40) cc_final: 0.8325 (tp40) REVERT: E 204 ASP cc_start: 0.8777 (m-30) cc_final: 0.8431 (m-30) REVERT: E 269 ASN cc_start: 0.7748 (m-40) cc_final: 0.7186 (m-40) REVERT: F 79 ASN cc_start: 0.7790 (t0) cc_final: 0.7457 (t0) REVERT: F 95 MET cc_start: 0.8456 (mmm) cc_final: 0.7968 (mmm) REVERT: F 129 LYS cc_start: 0.9137 (mttp) cc_final: 0.8893 (tppt) REVERT: F 176 GLN cc_start: 0.7405 (tm-30) cc_final: 0.7068 (tm-30) REVERT: F 203 GLN cc_start: 0.9020 (tp40) cc_final: 0.8192 (tp40) REVERT: F 204 ASP cc_start: 0.8891 (m-30) cc_final: 0.8449 (m-30) REVERT: F 226 ILE cc_start: 0.9006 (tp) cc_final: 0.8726 (tp) REVERT: F 227 ARG cc_start: 0.8507 (mmt90) cc_final: 0.8205 (mmt90) REVERT: F 228 GLN cc_start: 0.8601 (tt0) cc_final: 0.7969 (tm-30) REVERT: F 230 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7548 (mt-10) REVERT: F 243 LYS cc_start: 0.8763 (tmtt) cc_final: 0.8478 (tptp) REVERT: F 263 TRP cc_start: 0.8448 (m100) cc_final: 0.7929 (m100) REVERT: F 269 ASN cc_start: 0.8151 (m-40) cc_final: 0.7358 (m-40) REVERT: F 279 TRP cc_start: 0.7894 (t60) cc_final: 0.7572 (t-100) REVERT: G 46 THR cc_start: 0.8433 (t) cc_final: 0.7669 (p) REVERT: G 79 ASN cc_start: 0.8076 (t0) cc_final: 0.7734 (t0) REVERT: G 108 PHE cc_start: 0.9073 (p90) cc_final: 0.8621 (p90) REVERT: G 116 THR cc_start: 0.8845 (t) cc_final: 0.8451 (t) REVERT: G 117 GLN cc_start: 0.8322 (mm110) cc_final: 0.8049 (mm110) REVERT: G 149 PRO cc_start: 0.9017 (Cg_exo) cc_final: 0.8691 (Cg_endo) REVERT: G 179 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7412 (mt-10) REVERT: G 182 HIS cc_start: 0.8102 (m-70) cc_final: 0.7130 (m170) REVERT: G 203 GLN cc_start: 0.9127 (tp40) cc_final: 0.8104 (tp40) REVERT: G 204 ASP cc_start: 0.8893 (m-30) cc_final: 0.8674 (m-30) REVERT: G 213 ASP cc_start: 0.8728 (t0) cc_final: 0.8449 (t0) REVERT: G 227 ARG cc_start: 0.8486 (mmt90) cc_final: 0.7934 (mmt90) REVERT: G 228 GLN cc_start: 0.8563 (tt0) cc_final: 0.7972 (tm-30) REVERT: G 230 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7635 (mt-10) REVERT: G 238 LEU cc_start: 0.8812 (mt) cc_final: 0.8498 (mp) REVERT: G 241 ILE cc_start: 0.8983 (pt) cc_final: 0.8484 (pt) REVERT: G 242 GLN cc_start: 0.7980 (tp40) cc_final: 0.7570 (tp40) REVERT: G 260 ASP cc_start: 0.8123 (t0) cc_final: 0.7798 (t0) REVERT: G 261 LEU cc_start: 0.7977 (pt) cc_final: 0.7609 (pt) REVERT: G 263 TRP cc_start: 0.8227 (m100) cc_final: 0.7835 (m100) REVERT: G 266 ILE cc_start: 0.8637 (mp) cc_final: 0.8407 (mp) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.2911 time to fit residues: 190.4411 Evaluate side-chains 421 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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: 1.9990 chunk 67 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 123 optimal weight: 0.0070 chunk 90 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- 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 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 54 HIS D 117 GLN D 135 HIS D 228 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN A 228 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 HIS G 228 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.083317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.068476 restraints weight = 47180.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.071304 restraints weight = 27310.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.073282 restraints weight = 18217.048| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.561 16952 Z= 0.232 Angle : 0.913 12.063 23765 Z= 0.348 Chirality : 0.049 0.150 2128 Planarity : 0.005 0.042 2912 Dihedral : 18.288 89.885 2303 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.62 % Favored : 85.38 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 3.40 % 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: -2.26 (0.20), residues: 1792 helix: -1.91 (0.26), residues: 287 sheet: -1.78 (0.59), residues: 70 loop : -1.52 (0.18), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 279 HIS 0.011 0.001 HIS E 276 PHE 0.026 0.002 PHE F 108 TYR 0.015 0.002 TYR B 151 ARG 0.006 0.000 ARG E 197 Details of bonding type rmsd hydrogen bonds : bond 0.03078 ( 154) hydrogen bonds : angle 6.63012 ( 441) covalent geometry : bond 0.00652 (16772) covalent geometry : angle 0.91290 (23765) Misc. bond : bond 0.16603 ( 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 465 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 465 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 THR cc_start: 0.8145 (t) cc_final: 0.7528 (p) REVERT: B 60 LEU cc_start: 0.9067 (mm) cc_final: 0.8822 (mm) REVERT: B 63 GLN cc_start: 0.8865 (mt0) cc_final: 0.8489 (mt0) REVERT: B 79 ASN cc_start: 0.8037 (t0) cc_final: 0.7791 (t0) REVERT: B 95 MET cc_start: 0.8761 (mmm) cc_final: 0.8340 (mmm) REVERT: B 146 HIS cc_start: 0.8228 (p-80) cc_final: 0.7788 (p90) REVERT: B 151 TYR cc_start: 0.8764 (p90) cc_final: 0.8467 (p90) REVERT: B 176 GLN cc_start: 0.7261 (tm-30) cc_final: 0.7046 (tm-30) REVERT: B 203 GLN cc_start: 0.8925 (tp40) cc_final: 0.8288 (tp40) REVERT: B 204 ASP cc_start: 0.8877 (m-30) cc_final: 0.8430 (m-30) REVERT: B 227 ARG cc_start: 0.9208 (mtt180) cc_final: 0.8739 (mtt180) REVERT: B 230 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7857 (mt-10) REVERT: C 46 THR cc_start: 0.8487 (t) cc_final: 0.8171 (t) REVERT: C 51 LEU cc_start: 0.7432 (mt) cc_final: 0.7174 (mt) REVERT: C 90 THR cc_start: 0.8516 (p) cc_final: 0.8294 (t) REVERT: C 95 MET cc_start: 0.8682 (mmp) cc_final: 0.8406 (mmp) REVERT: C 108 PHE cc_start: 0.8990 (p90) cc_final: 0.8663 (p90) REVERT: C 139 ILE cc_start: 0.8706 (tp) cc_final: 0.8504 (tp) REVERT: C 149 PRO cc_start: 0.8840 (Cg_exo) cc_final: 0.8353 (Cg_endo) REVERT: C 179 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7516 (mt-10) REVERT: C 182 HIS cc_start: 0.8375 (m-70) cc_final: 0.7424 (m170) REVERT: C 203 GLN cc_start: 0.8775 (tp40) cc_final: 0.7731 (tp40) REVERT: C 204 ASP cc_start: 0.8887 (m-30) cc_final: 0.8543 (m-30) REVERT: C 227 ARG cc_start: 0.8569 (mtt180) cc_final: 0.8029 (mtt180) REVERT: C 228 GLN cc_start: 0.8490 (tt0) cc_final: 0.8071 (tm-30) REVERT: C 230 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7564 (mt-10) REVERT: C 255 LYS cc_start: 0.8671 (ptpp) cc_final: 0.8404 (ptpp) REVERT: C 269 ASN cc_start: 0.7445 (m-40) cc_final: 0.6838 (m-40) REVERT: D 90 THR cc_start: 0.8672 (p) cc_final: 0.8466 (t) REVERT: D 108 PHE cc_start: 0.9022 (p90) cc_final: 0.8424 (p90) REVERT: D 129 LYS cc_start: 0.9172 (mmtm) cc_final: 0.8877 (tppt) REVERT: D 133 TYR cc_start: 0.8774 (t80) cc_final: 0.8556 (t80) REVERT: D 135 HIS cc_start: 0.7620 (p90) cc_final: 0.7398 (p-80) REVERT: D 179 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7491 (mt-10) REVERT: D 183 GLN cc_start: 0.7215 (pm20) cc_final: 0.6570 (pm20) REVERT: D 197 ARG cc_start: 0.6416 (ttt180) cc_final: 0.6084 (ttt180) REVERT: D 200 PHE cc_start: 0.8247 (m-10) cc_final: 0.7425 (m-10) REVERT: D 203 GLN cc_start: 0.8781 (tp40) cc_final: 0.8079 (tp40) REVERT: D 204 ASP cc_start: 0.8893 (m-30) cc_final: 0.8086 (t0) REVERT: D 213 ASP cc_start: 0.8627 (t0) cc_final: 0.8382 (t0) REVERT: D 216 LEU cc_start: 0.9005 (tt) cc_final: 0.8772 (tt) REVERT: D 226 ILE cc_start: 0.9072 (tp) cc_final: 0.8825 (tp) REVERT: D 230 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7698 (mt-10) REVERT: D 238 LEU cc_start: 0.8986 (mt) cc_final: 0.8775 (mt) REVERT: D 242 GLN cc_start: 0.8267 (tp40) cc_final: 0.8018 (tp40) REVERT: D 260 ASP cc_start: 0.8140 (t0) cc_final: 0.7910 (t0) REVERT: D 261 LEU cc_start: 0.8472 (pt) cc_final: 0.8133 (pt) REVERT: D 269 ASN cc_start: 0.7723 (m-40) cc_final: 0.7173 (m-40) REVERT: A 54 HIS cc_start: 0.7569 (m-70) cc_final: 0.7062 (m-70) REVERT: A 90 THR cc_start: 0.8609 (p) cc_final: 0.8378 (t) REVERT: A 107 ASP cc_start: 0.8358 (t70) cc_final: 0.7900 (t0) REVERT: A 108 PHE cc_start: 0.8852 (p90) cc_final: 0.8635 (p90) REVERT: A 129 LYS cc_start: 0.9274 (ptpp) cc_final: 0.9034 (mttm) REVERT: A 135 HIS cc_start: 0.7978 (p-80) cc_final: 0.7560 (p90) REVERT: A 146 HIS cc_start: 0.7815 (p90) cc_final: 0.7036 (p90) REVERT: A 176 GLN cc_start: 0.7673 (tm-30) cc_final: 0.7283 (tm-30) REVERT: A 203 GLN cc_start: 0.8804 (tp40) cc_final: 0.8273 (tp40) REVERT: A 204 ASP cc_start: 0.8920 (m-30) cc_final: 0.8642 (m-30) REVERT: A 213 ASP cc_start: 0.8530 (t0) cc_final: 0.8275 (t0) REVERT: A 236 ASN cc_start: 0.8693 (p0) cc_final: 0.8395 (t0) REVERT: A 260 ASP cc_start: 0.8058 (t0) cc_final: 0.7767 (t0) REVERT: A 261 LEU cc_start: 0.8354 (pt) cc_final: 0.8023 (pt) REVERT: A 269 ASN cc_start: 0.7792 (m-40) cc_final: 0.7250 (m-40) REVERT: E 46 THR cc_start: 0.8362 (t) cc_final: 0.7818 (p) REVERT: E 61 VAL cc_start: 0.9326 (m) cc_final: 0.9110 (p) REVERT: E 63 GLN cc_start: 0.8870 (mt0) cc_final: 0.8476 (mt0) REVERT: E 79 ASN cc_start: 0.8081 (t0) cc_final: 0.7692 (t0) REVERT: E 129 LYS cc_start: 0.9039 (ptpp) cc_final: 0.8797 (mttp) REVERT: E 133 TYR cc_start: 0.8822 (t80) cc_final: 0.8421 (t80) REVERT: E 135 HIS cc_start: 0.8033 (p-80) cc_final: 0.7658 (p-80) REVERT: E 148 ILE cc_start: 0.9191 (mm) cc_final: 0.8815 (mm) REVERT: E 176 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7545 (tm-30) REVERT: E 203 GLN cc_start: 0.8893 (tp40) cc_final: 0.8239 (tp40) REVERT: E 204 ASP cc_start: 0.8818 (m-30) cc_final: 0.8473 (m-30) REVERT: E 226 ILE cc_start: 0.9186 (tp) cc_final: 0.8883 (tp) REVERT: E 230 GLU cc_start: 0.8607 (tt0) cc_final: 0.8080 (tt0) REVERT: E 269 ASN cc_start: 0.8156 (m-40) cc_final: 0.7191 (m-40) REVERT: F 79 ASN cc_start: 0.7888 (t0) cc_final: 0.7529 (t0) REVERT: F 129 LYS cc_start: 0.9102 (mttp) cc_final: 0.8878 (tppt) REVERT: F 130 ASP cc_start: 0.8062 (t0) cc_final: 0.7856 (t0) REVERT: F 176 GLN cc_start: 0.6854 (tm-30) cc_final: 0.6471 (tm-30) REVERT: F 203 GLN cc_start: 0.8861 (tp40) cc_final: 0.8000 (tp40) REVERT: F 204 ASP cc_start: 0.8947 (m-30) cc_final: 0.8518 (m-30) REVERT: F 226 ILE cc_start: 0.9013 (tp) cc_final: 0.8730 (tp) REVERT: F 227 ARG cc_start: 0.8595 (mmt90) cc_final: 0.8376 (mmt90) REVERT: F 230 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7593 (mt-10) REVERT: F 243 LYS cc_start: 0.8796 (tmtt) cc_final: 0.8515 (tptp) REVERT: F 263 TRP cc_start: 0.8476 (m100) cc_final: 0.7934 (m100) REVERT: F 269 ASN cc_start: 0.7773 (m-40) cc_final: 0.7104 (m-40) REVERT: F 277 TRP cc_start: 0.7949 (t-100) cc_final: 0.7475 (t-100) REVERT: G 37 ILE cc_start: 0.8411 (pt) cc_final: 0.7932 (mt) REVERT: G 79 ASN cc_start: 0.8207 (t0) cc_final: 0.7844 (t0) REVERT: G 107 ASP cc_start: 0.8013 (t0) cc_final: 0.7757 (t0) REVERT: G 117 GLN cc_start: 0.8301 (mm110) cc_final: 0.8048 (mm110) REVERT: G 141 ASN cc_start: 0.8863 (t0) cc_final: 0.8602 (t0) REVERT: G 149 PRO cc_start: 0.9132 (Cg_exo) cc_final: 0.8748 (Cg_endo) REVERT: G 179 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7481 (mt-10) REVERT: G 182 HIS cc_start: 0.8189 (m-70) cc_final: 0.7464 (m170) REVERT: G 203 GLN cc_start: 0.8980 (tp40) cc_final: 0.7825 (tp40) REVERT: G 204 ASP cc_start: 0.8966 (m-30) cc_final: 0.8734 (m-30) REVERT: G 213 ASP cc_start: 0.8761 (t0) cc_final: 0.8521 (t0) REVERT: G 227 ARG cc_start: 0.8616 (mmt90) cc_final: 0.8042 (mmt90) REVERT: G 230 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7800 (mt-10) REVERT: G 238 LEU cc_start: 0.8767 (mt) cc_final: 0.8476 (mp) REVERT: G 241 ILE cc_start: 0.9020 (pt) cc_final: 0.8628 (pt) REVERT: G 244 ASP cc_start: 0.8245 (t0) cc_final: 0.8041 (t0) REVERT: G 260 ASP cc_start: 0.8179 (t0) cc_final: 0.7930 (t0) REVERT: G 261 LEU cc_start: 0.8049 (pt) cc_final: 0.7729 (pt) REVERT: G 263 TRP cc_start: 0.8278 (m100) cc_final: 0.7797 (m100) REVERT: G 269 ASN cc_start: 0.7858 (m-40) cc_final: 0.7249 (m-40) outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.2977 time to fit residues: 198.9636 Evaluate side-chains 428 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 1.536 ------------------------------------------------------------------------------- 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: 0.0670 chunk 90 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 154 optimal weight: 0.0870 chunk 159 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 133 optimal weight: 0.0570 chunk 114 optimal weight: 0.0170 chunk 124 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 overall best weight: 0.1652 ------------------------------------------------------------------------------- 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 228 GLN B 242 GLN C 228 GLN C 242 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN D 228 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN F 117 GLN F 228 GLN F 242 GLN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 HIS G 228 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.088546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.073038 restraints weight = 44673.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.076160 restraints weight = 24936.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.078365 restraints weight = 16193.467| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.368 16952 Z= 0.147 Angle : 0.847 10.894 23765 Z= 0.331 Chirality : 0.047 0.221 2128 Planarity : 0.004 0.040 2912 Dihedral : 17.895 88.854 2303 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.56 % Favored : 87.44 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: -2.07 (0.20), residues: 1792 helix: -2.02 (0.26), residues: 287 sheet: None (None), residues: 0 loop : -1.36 (0.17), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 279 HIS 0.006 0.001 HIS E 276 PHE 0.012 0.001 PHE E 108 TYR 0.010 0.001 TYR A 133 ARG 0.005 0.001 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.03111 ( 154) hydrogen bonds : angle 6.60085 ( 441) covalent geometry : bond 0.00381 (16772) covalent geometry : angle 0.84671 (23765) Misc. bond : bond 0.09585 ( 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 453 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLN cc_start: 0.8724 (mt0) cc_final: 0.8393 (mt0) REVERT: B 95 MET cc_start: 0.8673 (mmm) cc_final: 0.8371 (mmp) REVERT: B 146 HIS cc_start: 0.8172 (p-80) cc_final: 0.7816 (p90) REVERT: B 176 GLN cc_start: 0.7419 (tm-30) cc_final: 0.7190 (tm-30) REVERT: B 200 PHE cc_start: 0.8107 (m-10) cc_final: 0.7104 (m-10) REVERT: B 203 GLN cc_start: 0.8823 (tp40) cc_final: 0.8082 (tp40) REVERT: B 204 ASP cc_start: 0.8736 (m-30) cc_final: 0.7597 (t0) REVERT: B 228 GLN cc_start: 0.8508 (tt0) cc_final: 0.7848 (tm-30) REVERT: B 255 LYS cc_start: 0.8839 (ptpp) cc_final: 0.8621 (ptpp) REVERT: B 277 TRP cc_start: 0.8457 (t-100) cc_final: 0.8218 (t-100) REVERT: C 46 THR cc_start: 0.7630 (t) cc_final: 0.7370 (t) REVERT: C 90 THR cc_start: 0.8512 (p) cc_final: 0.8267 (t) REVERT: C 135 HIS cc_start: 0.7423 (p90) cc_final: 0.7062 (p90) REVERT: C 149 PRO cc_start: 0.8853 (Cg_exo) cc_final: 0.8308 (Cg_endo) REVERT: C 179 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7184 (mt-10) REVERT: C 182 HIS cc_start: 0.8158 (m-70) cc_final: 0.7082 (m170) REVERT: C 183 GLN cc_start: 0.6609 (pm20) cc_final: 0.6037 (pm20) REVERT: C 203 GLN cc_start: 0.8737 (tp40) cc_final: 0.7729 (tp40) REVERT: C 204 ASP cc_start: 0.8803 (m-30) cc_final: 0.8418 (m-30) REVERT: C 238 LEU cc_start: 0.8930 (mp) cc_final: 0.8512 (mp) REVERT: C 255 LYS cc_start: 0.8739 (ptpp) cc_final: 0.8471 (ptpp) REVERT: C 269 ASN cc_start: 0.7334 (m-40) cc_final: 0.6693 (m-40) REVERT: D 108 PHE cc_start: 0.8951 (p90) cc_final: 0.8558 (p90) REVERT: D 129 LYS cc_start: 0.9150 (mmtm) cc_final: 0.8835 (tppt) REVERT: D 133 TYR cc_start: 0.8638 (t80) cc_final: 0.8410 (t80) REVERT: D 179 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7107 (mt-10) REVERT: D 183 GLN cc_start: 0.6915 (pm20) cc_final: 0.6330 (pm20) REVERT: D 203 GLN cc_start: 0.8752 (tp40) cc_final: 0.8092 (tp40) REVERT: D 204 ASP cc_start: 0.8788 (m-30) cc_final: 0.8429 (m-30) REVERT: D 213 ASP cc_start: 0.8579 (t0) cc_final: 0.8232 (t0) REVERT: D 226 ILE cc_start: 0.9012 (tp) cc_final: 0.8766 (tp) REVERT: D 227 ARG cc_start: 0.8523 (mmt90) cc_final: 0.8256 (mmt180) REVERT: D 228 GLN cc_start: 0.8290 (tt0) cc_final: 0.7670 (tm-30) REVERT: D 230 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7403 (mt-10) REVERT: D 242 GLN cc_start: 0.8313 (tp40) cc_final: 0.7995 (tp40) REVERT: D 260 ASP cc_start: 0.8032 (t0) cc_final: 0.7777 (t0) REVERT: D 261 LEU cc_start: 0.8256 (pt) cc_final: 0.7846 (pt) REVERT: D 269 ASN cc_start: 0.7483 (m-40) cc_final: 0.6963 (m-40) REVERT: A 37 ILE cc_start: 0.8464 (pt) cc_final: 0.8126 (pt) REVERT: A 54 HIS cc_start: 0.7592 (m-70) cc_final: 0.7117 (m-70) REVERT: A 79 ASN cc_start: 0.7578 (t0) cc_final: 0.7119 (t0) REVERT: A 107 ASP cc_start: 0.8175 (t70) cc_final: 0.7915 (t0) REVERT: A 108 PHE cc_start: 0.8762 (p90) cc_final: 0.8161 (p90) REVERT: A 129 LYS cc_start: 0.9251 (ptpp) cc_final: 0.9022 (mttm) REVERT: A 135 HIS cc_start: 0.7742 (p-80) cc_final: 0.7307 (p90) REVERT: A 148 ILE cc_start: 0.8606 (mm) cc_final: 0.8405 (mm) REVERT: A 176 GLN cc_start: 0.7508 (tm-30) cc_final: 0.7093 (tm-30) REVERT: A 203 GLN cc_start: 0.8749 (tp40) cc_final: 0.8273 (tp40) REVERT: A 213 ASP cc_start: 0.8464 (t0) cc_final: 0.8172 (t0) REVERT: A 227 ARG cc_start: 0.9104 (mtt180) cc_final: 0.8437 (mmm160) REVERT: A 230 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7386 (tm-30) REVERT: A 260 ASP cc_start: 0.7933 (t0) cc_final: 0.7678 (t0) REVERT: A 261 LEU cc_start: 0.8140 (pt) cc_final: 0.7844 (pt) REVERT: A 269 ASN cc_start: 0.7529 (m-40) cc_final: 0.6819 (m-40) REVERT: E 63 GLN cc_start: 0.8851 (mt0) cc_final: 0.8344 (mp10) REVERT: E 79 ASN cc_start: 0.8012 (t0) cc_final: 0.7572 (t0) REVERT: E 108 PHE cc_start: 0.8928 (p90) cc_final: 0.8600 (p90) REVERT: E 133 TYR cc_start: 0.8676 (t80) cc_final: 0.8287 (t80) REVERT: E 135 HIS cc_start: 0.7901 (p-80) cc_final: 0.7596 (p90) REVERT: E 148 ILE cc_start: 0.9095 (mm) cc_final: 0.8838 (mm) REVERT: E 176 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7570 (tm-30) REVERT: E 203 GLN cc_start: 0.8925 (tp40) cc_final: 0.8264 (tp40) REVERT: E 204 ASP cc_start: 0.8734 (m-30) cc_final: 0.8372 (m-30) REVERT: E 269 ASN cc_start: 0.7676 (m-40) cc_final: 0.7202 (m-40) REVERT: F 54 HIS cc_start: 0.7362 (m-70) cc_final: 0.7124 (m-70) REVERT: F 62 GLN cc_start: 0.8680 (mm110) cc_final: 0.8297 (mm-40) REVERT: F 79 ASN cc_start: 0.7655 (t0) cc_final: 0.7251 (t0) REVERT: F 129 LYS cc_start: 0.9117 (mttp) cc_final: 0.8902 (tppt) REVERT: F 130 ASP cc_start: 0.8030 (t0) cc_final: 0.7810 (t0) REVERT: F 179 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7245 (mt-10) REVERT: F 204 ASP cc_start: 0.8826 (m-30) cc_final: 0.8404 (m-30) REVERT: F 226 ILE cc_start: 0.8878 (tp) cc_final: 0.8613 (tp) REVERT: F 227 ARG cc_start: 0.8475 (mmt90) cc_final: 0.8249 (mmt90) REVERT: F 228 GLN cc_start: 0.8488 (tt0) cc_final: 0.8077 (tm-30) REVERT: F 230 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7631 (mt-10) REVERT: F 238 LEU cc_start: 0.9023 (mt) cc_final: 0.8818 (mt) REVERT: F 243 LYS cc_start: 0.8746 (tmtt) cc_final: 0.8467 (tptp) REVERT: F 263 TRP cc_start: 0.8358 (m100) cc_final: 0.7864 (m100) REVERT: F 269 ASN cc_start: 0.8108 (m-40) cc_final: 0.7269 (m-40) REVERT: F 277 TRP cc_start: 0.7926 (t-100) cc_final: 0.7395 (t-100) REVERT: G 54 HIS cc_start: 0.7579 (m-70) cc_final: 0.7315 (m-70) REVERT: G 79 ASN cc_start: 0.8219 (t0) cc_final: 0.7789 (t0) REVERT: G 116 THR cc_start: 0.8795 (t) cc_final: 0.8378 (t) REVERT: G 117 GLN cc_start: 0.8385 (mm110) cc_final: 0.8152 (mm110) REVERT: G 129 LYS cc_start: 0.9290 (mttm) cc_final: 0.8969 (tppt) REVERT: G 130 ASP cc_start: 0.8203 (t0) cc_final: 0.7926 (t0) REVERT: G 149 PRO cc_start: 0.9073 (Cg_exo) cc_final: 0.8659 (Cg_endo) REVERT: G 179 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7176 (mt-10) REVERT: G 182 HIS cc_start: 0.8041 (m-70) cc_final: 0.7325 (m170) REVERT: G 183 GLN cc_start: 0.6192 (pm20) cc_final: 0.5784 (pm20) REVERT: G 203 GLN cc_start: 0.8891 (tp40) cc_final: 0.7749 (tp40) REVERT: G 204 ASP cc_start: 0.8832 (m-30) cc_final: 0.7799 (t0) REVERT: G 213 ASP cc_start: 0.8704 (t0) cc_final: 0.8341 (t0) REVERT: G 226 ILE cc_start: 0.8963 (tp) cc_final: 0.8716 (tp) REVERT: G 227 ARG cc_start: 0.8467 (mmt90) cc_final: 0.7884 (mmt90) REVERT: G 228 GLN cc_start: 0.8520 (tt0) cc_final: 0.7856 (tm-30) REVERT: G 230 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7559 (mt-10) REVERT: G 241 ILE cc_start: 0.9033 (pt) cc_final: 0.8809 (pt) REVERT: G 260 ASP cc_start: 0.8093 (t0) cc_final: 0.7800 (t0) REVERT: G 261 LEU cc_start: 0.7860 (pt) cc_final: 0.7516 (pt) REVERT: G 263 TRP cc_start: 0.8122 (m100) cc_final: 0.7727 (m100) REVERT: G 269 ASN cc_start: 0.7677 (m-40) cc_final: 0.7077 (m-40) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.2929 time to fit residues: 191.4639 Evaluate side-chains 419 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 1.718 ------------------------------------------------------------------------------- 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: 0.0370 chunk 86 optimal weight: 1.9990 chunk 162 optimal weight: 0.0170 chunk 143 optimal weight: 0.0470 chunk 164 optimal weight: 0.0470 chunk 62 optimal weight: 4.9990 chunk 130 optimal weight: 0.0980 chunk 113 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 overall best weight: 0.0470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS B 117 GLN B 228 GLN C 228 GLN D 117 GLN D 135 HIS D 146 HIS D 228 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN A 273 GLN E 54 HIS E 117 GLN ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS E 228 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.093079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.077712 restraints weight = 44366.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.080982 restraints weight = 24279.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.083274 restraints weight = 15544.015| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.316 16952 Z= 0.137 Angle : 0.833 9.422 23765 Z= 0.329 Chirality : 0.046 0.158 2128 Planarity : 0.004 0.031 2912 Dihedral : 17.510 89.932 2303 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 0.06 % Allowed : 0.84 % Favored : 99.10 % 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: -2.04 (0.21), residues: 1792 helix: -2.05 (0.25), residues: 301 sheet: None (None), residues: 0 loop : -1.31 (0.18), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 270 HIS 0.007 0.001 HIS E 182 PHE 0.021 0.001 PHE B 108 TYR 0.013 0.001 TYR B 133 ARG 0.004 0.001 ARG E 109 Details of bonding type rmsd hydrogen bonds : bond 0.02946 ( 154) hydrogen bonds : angle 6.63606 ( 441) covalent geometry : bond 0.00359 (16772) covalent geometry : angle 0.83297 (23765) Misc. bond : bond 0.06955 ( 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 444 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 443 time to evaluate : 1.579 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 60 LEU cc_start: 0.8917 (mm) cc_final: 0.8572 (mt) REVERT: B 62 GLN cc_start: 0.8607 (tp40) cc_final: 0.8377 (tp40) REVERT: B 63 GLN cc_start: 0.8613 (mt0) cc_final: 0.8353 (mt0) REVERT: B 67 LEU cc_start: 0.8994 (tp) cc_final: 0.8791 (tp) REVERT: B 79 ASN cc_start: 0.7842 (t0) cc_final: 0.7482 (t0) REVERT: B 146 HIS cc_start: 0.8215 (p-80) cc_final: 0.7925 (p90) REVERT: B 149 PRO cc_start: 0.8792 (Cg_exo) cc_final: 0.8358 (Cg_endo) REVERT: B 176 GLN cc_start: 0.7259 (tm-30) cc_final: 0.6776 (tm-30) REVERT: B 203 GLN cc_start: 0.8847 (tp40) cc_final: 0.8509 (tp40) REVERT: B 204 ASP cc_start: 0.8627 (m-30) cc_final: 0.7696 (t0) REVERT: B 255 LYS cc_start: 0.8894 (ptpp) cc_final: 0.8649 (ptpp) REVERT: B 279 TRP cc_start: 0.7634 (t-100) cc_final: 0.7001 (t-100) REVERT: C 63 GLN cc_start: 0.8531 (pt0) cc_final: 0.8299 (mp10) REVERT: C 109 ARG cc_start: 0.9044 (mmt180) cc_final: 0.8708 (mmp80) REVERT: C 135 HIS cc_start: 0.7309 (p90) cc_final: 0.7101 (p90) REVERT: C 139 ILE cc_start: 0.8873 (tp) cc_final: 0.8672 (tp) REVERT: C 149 PRO cc_start: 0.8542 (Cg_exo) cc_final: 0.8310 (Cg_endo) REVERT: C 179 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7026 (mt-10) REVERT: C 182 HIS cc_start: 0.7928 (m-70) cc_final: 0.7153 (m170) REVERT: C 200 PHE cc_start: 0.7838 (m-80) cc_final: 0.7024 (m-10) REVERT: C 203 GLN cc_start: 0.8733 (tp40) cc_final: 0.7713 (tp40) REVERT: C 204 ASP cc_start: 0.8692 (m-30) cc_final: 0.7595 (t0) REVERT: C 228 GLN cc_start: 0.8423 (tt0) cc_final: 0.7845 (tm-30) REVERT: C 255 LYS cc_start: 0.8803 (ptpp) cc_final: 0.8480 (ptpp) REVERT: C 269 ASN cc_start: 0.7355 (m-40) cc_final: 0.6741 (m-40) REVERT: D 46 THR cc_start: 0.7417 (t) cc_final: 0.7127 (t) REVERT: D 108 PHE cc_start: 0.8969 (p90) cc_final: 0.8686 (p90) REVERT: D 129 LYS cc_start: 0.9063 (mmtm) cc_final: 0.8767 (tppt) REVERT: D 179 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7039 (mt-10) REVERT: D 183 GLN cc_start: 0.6671 (pm20) cc_final: 0.6097 (pm20) REVERT: D 203 GLN cc_start: 0.8740 (tp40) cc_final: 0.8152 (tp40) REVERT: D 204 ASP cc_start: 0.8672 (m-30) cc_final: 0.7729 (t0) REVERT: D 213 ASP cc_start: 0.8563 (t0) cc_final: 0.8320 (t0) REVERT: D 226 ILE cc_start: 0.9026 (tp) cc_final: 0.8823 (tp) REVERT: D 230 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7351 (mt-10) REVERT: D 260 ASP cc_start: 0.7915 (t0) cc_final: 0.7664 (t0) REVERT: D 261 LEU cc_start: 0.8115 (pt) cc_final: 0.7749 (pt) REVERT: D 269 ASN cc_start: 0.7476 (m-40) cc_final: 0.6955 (m-40) REVERT: D 271 ASP cc_start: 0.7881 (p0) cc_final: 0.7578 (p0) REVERT: A 54 HIS cc_start: 0.7531 (m-70) cc_final: 0.7060 (m-70) REVERT: A 62 GLN cc_start: 0.8759 (mm110) cc_final: 0.8425 (mm110) REVERT: A 63 GLN cc_start: 0.8333 (pm20) cc_final: 0.8078 (pm20) REVERT: A 79 ASN cc_start: 0.7694 (t0) cc_final: 0.7198 (t0) REVERT: A 107 ASP cc_start: 0.8061 (t70) cc_final: 0.7724 (t0) REVERT: A 129 LYS cc_start: 0.9256 (ptpp) cc_final: 0.9015 (mttm) REVERT: A 135 HIS cc_start: 0.7570 (p-80) cc_final: 0.7365 (p90) REVERT: A 169 ASP cc_start: 0.7082 (t0) cc_final: 0.6597 (p0) REVERT: A 176 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7286 (tm-30) REVERT: A 200 PHE cc_start: 0.7976 (m-80) cc_final: 0.7043 (m-10) REVERT: A 203 GLN cc_start: 0.8688 (tp40) cc_final: 0.8223 (tp40) REVERT: A 204 ASP cc_start: 0.8768 (m-30) cc_final: 0.7710 (t0) REVERT: A 213 ASP cc_start: 0.8396 (t0) cc_final: 0.8105 (t0) REVERT: A 230 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7313 (tm-30) REVERT: A 260 ASP cc_start: 0.7656 (t0) cc_final: 0.7440 (t0) REVERT: A 269 ASN cc_start: 0.7435 (m-40) cc_final: 0.6823 (m-40) REVERT: E 63 GLN cc_start: 0.8773 (mt0) cc_final: 0.8310 (mt0) REVERT: E 79 ASN cc_start: 0.7825 (t0) cc_final: 0.7306 (t0) REVERT: E 106 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8462 (tm-30) REVERT: E 135 HIS cc_start: 0.7769 (p-80) cc_final: 0.7400 (p-80) REVERT: E 139 ILE cc_start: 0.9110 (tp) cc_final: 0.8896 (tp) REVERT: E 176 GLN cc_start: 0.7707 (tm-30) cc_final: 0.7069 (tm-30) REVERT: E 203 GLN cc_start: 0.8962 (tp40) cc_final: 0.8317 (tp40) REVERT: E 204 ASP cc_start: 0.8705 (m-30) cc_final: 0.7694 (t0) REVERT: E 227 ARG cc_start: 0.8600 (mtt180) cc_final: 0.8264 (mmm160) REVERT: E 228 GLN cc_start: 0.7731 (tm130) cc_final: 0.7210 (tm-30) REVERT: E 269 ASN cc_start: 0.7571 (m-40) cc_final: 0.7081 (m-40) REVERT: F 54 HIS cc_start: 0.7216 (m-70) cc_final: 0.6974 (m-70) REVERT: F 79 ASN cc_start: 0.7536 (t0) cc_final: 0.7209 (t0) REVERT: F 109 ARG cc_start: 0.8695 (mmm160) cc_final: 0.8283 (tpp-160) REVERT: F 129 LYS cc_start: 0.9165 (mttp) cc_final: 0.8863 (tppt) REVERT: F 176 GLN cc_start: 0.7059 (tm-30) cc_final: 0.6599 (tm-30) REVERT: F 203 GLN cc_start: 0.8788 (tp40) cc_final: 0.8078 (tp40) REVERT: F 226 ILE cc_start: 0.8898 (tp) cc_final: 0.8690 (tp) REVERT: F 230 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7715 (mt-10) REVERT: F 243 LYS cc_start: 0.8729 (tmtt) cc_final: 0.8489 (tptp) REVERT: F 263 TRP cc_start: 0.8204 (m100) cc_final: 0.7840 (m100) REVERT: F 269 ASN cc_start: 0.7550 (m-40) cc_final: 0.6854 (m-40) REVERT: F 277 TRP cc_start: 0.7868 (t-100) cc_final: 0.7351 (t-100) REVERT: F 279 TRP cc_start: 0.7722 (t60) cc_final: 0.7375 (t60) REVERT: G 46 THR cc_start: 0.7658 (t) cc_final: 0.7239 (t) REVERT: G 79 ASN cc_start: 0.8115 (t0) cc_final: 0.7622 (t0) REVERT: G 107 ASP cc_start: 0.8375 (t70) cc_final: 0.7992 (t0) REVERT: G 112 PHE cc_start: 0.7164 (m-80) cc_final: 0.6871 (m-80) REVERT: G 129 LYS cc_start: 0.9286 (mttm) cc_final: 0.9026 (tppp) REVERT: G 130 ASP cc_start: 0.8091 (t0) cc_final: 0.7884 (t0) REVERT: G 135 HIS cc_start: 0.7427 (p90) cc_final: 0.7167 (p-80) REVERT: G 149 PRO cc_start: 0.8916 (Cg_exo) cc_final: 0.8530 (Cg_endo) REVERT: G 176 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7292 (tm-30) REVERT: G 203 GLN cc_start: 0.8883 (tp40) cc_final: 0.8456 (tp40) REVERT: G 204 ASP cc_start: 0.8700 (m-30) cc_final: 0.7938 (t70) REVERT: G 213 ASP cc_start: 0.8638 (t0) cc_final: 0.8293 (t0) REVERT: G 227 ARG cc_start: 0.8413 (mmt90) cc_final: 0.7922 (mmt90) REVERT: G 230 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7491 (mt-10) REVERT: G 260 ASP cc_start: 0.8029 (t0) cc_final: 0.7795 (t0) REVERT: G 261 LEU cc_start: 0.7713 (pt) cc_final: 0.7420 (pt) REVERT: G 263 TRP cc_start: 0.7956 (m100) cc_final: 0.7726 (m100) REVERT: G 269 ASN cc_start: 0.7644 (m-40) cc_final: 0.7172 (m-40) outliers start: 1 outliers final: 0 residues processed: 444 average time/residue: 0.2931 time to fit residues: 187.5185 Evaluate side-chains 408 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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: 1.9990 chunk 47 optimal weight: 0.6980 chunk 163 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 164 optimal weight: 0.4980 chunk 94 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN B 135 HIS B 228 GLN C 62 GLN C 63 GLN C 146 HIS C 228 GLN D 146 HIS D 273 GLN A 146 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 HIS ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 HIS G 228 GLN G 273 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.086746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.071889 restraints weight = 46517.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.074879 restraints weight = 26006.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.076972 restraints weight = 17017.080| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.523 16952 Z= 0.211 Angle : 0.901 12.774 23765 Z= 0.350 Chirality : 0.049 0.149 2128 Planarity : 0.005 0.049 2912 Dihedral : 17.910 89.473 2303 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -2.24 (0.20), residues: 1792 helix: -1.87 (0.26), residues: 294 sheet: -2.43 (0.54), residues: 70 loop : -1.46 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 277 HIS 0.012 0.001 HIS G 276 PHE 0.019 0.002 PHE G 108 TYR 0.013 0.002 TYR B 151 ARG 0.011 0.001 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.02998 ( 154) hydrogen bonds : angle 6.81453 ( 441) covalent geometry : bond 0.00602 (16772) covalent geometry : angle 0.90123 (23765) Misc. bond : bond 0.14310 ( 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 463 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 463 time to evaluate : 1.675 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 54 HIS cc_start: 0.6932 (m170) cc_final: 0.6694 (m-70) REVERT: B 61 VAL cc_start: 0.9179 (m) cc_final: 0.8976 (p) REVERT: B 63 GLN cc_start: 0.8745 (mt0) cc_final: 0.8435 (mt0) REVERT: B 95 MET cc_start: 0.8626 (mmp) cc_final: 0.8262 (mmm) REVERT: B 108 PHE cc_start: 0.8960 (p90) cc_final: 0.8647 (p90) REVERT: B 129 LYS cc_start: 0.9244 (tppt) cc_final: 0.8984 (tppp) REVERT: B 135 HIS cc_start: 0.7552 (p90) cc_final: 0.7070 (p-80) REVERT: B 146 HIS cc_start: 0.8186 (p-80) cc_final: 0.7844 (p90) REVERT: B 149 PRO cc_start: 0.8968 (Cg_exo) cc_final: 0.8608 (Cg_endo) REVERT: B 151 TYR cc_start: 0.8738 (p90) cc_final: 0.8536 (p90) REVERT: B 176 GLN cc_start: 0.6981 (tm-30) cc_final: 0.6662 (tm-30) REVERT: B 203 GLN cc_start: 0.8862 (tp40) cc_final: 0.8259 (tp40) REVERT: B 204 ASP cc_start: 0.8770 (m-30) cc_final: 0.7791 (t0) REVERT: B 228 GLN cc_start: 0.8437 (tt0) cc_final: 0.7773 (tm-30) REVERT: B 230 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7590 (mt-10) REVERT: B 255 LYS cc_start: 0.8879 (ptpp) cc_final: 0.8618 (pttm) REVERT: C 34 PHE cc_start: 0.8813 (p90) cc_final: 0.8309 (p90) REVERT: C 46 THR cc_start: 0.7987 (t) cc_final: 0.7738 (t) REVERT: C 108 PHE cc_start: 0.8992 (p90) cc_final: 0.8784 (p90) REVERT: C 135 HIS cc_start: 0.7358 (p90) cc_final: 0.6932 (p90) REVERT: C 149 PRO cc_start: 0.8724 (Cg_exo) cc_final: 0.8471 (Cg_endo) REVERT: C 179 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6773 (mt-10) REVERT: C 182 HIS cc_start: 0.8281 (m-70) cc_final: 0.7406 (m170) REVERT: C 203 GLN cc_start: 0.8806 (tp40) cc_final: 0.7744 (tp40) REVERT: C 204 ASP cc_start: 0.8800 (m-30) cc_final: 0.8375 (m-30) REVERT: C 227 ARG cc_start: 0.8932 (mtt180) cc_final: 0.8596 (mtt180) REVERT: C 238 LEU cc_start: 0.8939 (mt) cc_final: 0.8574 (mp) REVERT: C 255 LYS cc_start: 0.8723 (ptpp) cc_final: 0.8441 (ptpp) REVERT: C 269 ASN cc_start: 0.7447 (m-40) cc_final: 0.6918 (m-40) REVERT: D 46 THR cc_start: 0.7937 (t) cc_final: 0.7659 (t) REVERT: D 51 LEU cc_start: 0.7408 (mt) cc_final: 0.7190 (mt) REVERT: D 108 PHE cc_start: 0.9079 (p90) cc_final: 0.8366 (p90) REVERT: D 129 LYS cc_start: 0.9231 (mmtm) cc_final: 0.8916 (tppt) REVERT: D 149 PRO cc_start: 0.8998 (Cg_exo) cc_final: 0.7911 (Cg_endo) REVERT: D 179 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7213 (mt-10) REVERT: D 182 HIS cc_start: 0.8041 (m170) cc_final: 0.7111 (m-70) REVERT: D 183 GLN cc_start: 0.6195 (pm20) cc_final: 0.5693 (pm20) REVERT: D 203 GLN cc_start: 0.8797 (tp40) cc_final: 0.8122 (tp40) REVERT: D 204 ASP cc_start: 0.8790 (m-30) cc_final: 0.7981 (t0) REVERT: D 213 ASP cc_start: 0.8658 (t0) cc_final: 0.8295 (t0) REVERT: D 230 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7484 (mt-10) REVERT: D 238 LEU cc_start: 0.8975 (mt) cc_final: 0.8723 (mt) REVERT: D 255 LYS cc_start: 0.8684 (pttm) cc_final: 0.8468 (ptpp) REVERT: D 261 LEU cc_start: 0.8188 (pt) cc_final: 0.7955 (pt) REVERT: D 269 ASN cc_start: 0.7736 (m-40) cc_final: 0.7183 (m-40) REVERT: D 271 ASP cc_start: 0.7981 (p0) cc_final: 0.7721 (p0) REVERT: A 54 HIS cc_start: 0.7642 (m-70) cc_final: 0.7131 (m-70) REVERT: A 62 GLN cc_start: 0.8807 (mm110) cc_final: 0.8440 (mm-40) REVERT: A 63 GLN cc_start: 0.8395 (pm20) cc_final: 0.8047 (pm20) REVERT: A 79 ASN cc_start: 0.7730 (t0) cc_final: 0.7450 (t0) REVERT: A 90 THR cc_start: 0.8708 (p) cc_final: 0.8475 (t) REVERT: A 95 MET cc_start: 0.9074 (mmm) cc_final: 0.8592 (mmm) REVERT: A 107 ASP cc_start: 0.8173 (t70) cc_final: 0.7935 (t0) REVERT: A 129 LYS cc_start: 0.9262 (ptpp) cc_final: 0.9042 (mttm) REVERT: A 135 HIS cc_start: 0.7800 (p-80) cc_final: 0.7543 (p90) REVERT: A 176 GLN cc_start: 0.7462 (tm-30) cc_final: 0.6887 (tm-30) REVERT: A 213 ASP cc_start: 0.8473 (t0) cc_final: 0.8199 (t0) REVERT: A 230 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7329 (tm-30) REVERT: A 260 ASP cc_start: 0.7827 (t0) cc_final: 0.7588 (t0) REVERT: A 261 LEU cc_start: 0.8205 (pt) cc_final: 0.7915 (pt) REVERT: A 269 ASN cc_start: 0.8079 (m-40) cc_final: 0.7288 (m-40) REVERT: E 63 GLN cc_start: 0.8893 (mt0) cc_final: 0.8429 (mt0) REVERT: E 79 ASN cc_start: 0.7977 (t0) cc_final: 0.7559 (t0) REVERT: E 108 PHE cc_start: 0.8753 (p90) cc_final: 0.8430 (p90) REVERT: E 129 LYS cc_start: 0.9062 (ptpp) cc_final: 0.8831 (mttp) REVERT: E 133 TYR cc_start: 0.8715 (t80) cc_final: 0.8326 (t80) REVERT: E 135 HIS cc_start: 0.7939 (p-80) cc_final: 0.7627 (p-80) REVERT: E 176 GLN cc_start: 0.7620 (tm-30) cc_final: 0.7101 (tm-30) REVERT: E 203 GLN cc_start: 0.8831 (tp40) cc_final: 0.8160 (tp40) REVERT: E 204 ASP cc_start: 0.8783 (m-30) cc_final: 0.7751 (t0) REVERT: E 227 ARG cc_start: 0.8724 (mtt180) cc_final: 0.8275 (mmm160) REVERT: E 269 ASN cc_start: 0.7877 (m-40) cc_final: 0.7189 (t0) REVERT: F 54 HIS cc_start: 0.7515 (m-70) cc_final: 0.7272 (m-70) REVERT: F 63 GLN cc_start: 0.8575 (pt0) cc_final: 0.8284 (mp10) REVERT: F 79 ASN cc_start: 0.7787 (t0) cc_final: 0.7476 (t0) REVERT: F 129 LYS cc_start: 0.9166 (mttp) cc_final: 0.8929 (tppt) REVERT: F 130 ASP cc_start: 0.8080 (t0) cc_final: 0.7848 (t0) REVERT: F 176 GLN cc_start: 0.7120 (tm-30) cc_final: 0.6502 (tm-30) REVERT: F 179 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7628 (mt-10) REVERT: F 203 GLN cc_start: 0.8843 (tp40) cc_final: 0.7892 (tp40) REVERT: F 204 ASP cc_start: 0.8857 (m-30) cc_final: 0.8394 (m-30) REVERT: F 228 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7679 (tm-30) REVERT: F 230 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7801 (mt-10) REVERT: F 243 LYS cc_start: 0.8767 (tmtt) cc_final: 0.8475 (tptp) REVERT: F 263 TRP cc_start: 0.8395 (m100) cc_final: 0.7924 (m100) REVERT: F 269 ASN cc_start: 0.8180 (m-40) cc_final: 0.7327 (m-40) REVERT: F 277 TRP cc_start: 0.7950 (t-100) cc_final: 0.7391 (t-100) REVERT: F 279 TRP cc_start: 0.7928 (t60) cc_final: 0.7498 (t60) REVERT: G 54 HIS cc_start: 0.7534 (m-70) cc_final: 0.7189 (m-70) REVERT: G 107 ASP cc_start: 0.8177 (t70) cc_final: 0.7822 (t0) REVERT: G 129 LYS cc_start: 0.9286 (mttm) cc_final: 0.9015 (tppt) REVERT: G 149 PRO cc_start: 0.9004 (Cg_exo) cc_final: 0.8651 (Cg_endo) REVERT: G 159 MET cc_start: 0.3094 (tpt) cc_final: 0.2725 (tpt) REVERT: G 179 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7014 (mt-10) REVERT: G 183 GLN cc_start: 0.7224 (pm20) cc_final: 0.6591 (pm20) REVERT: G 203 GLN cc_start: 0.8960 (tp40) cc_final: 0.7740 (tp40) REVERT: G 204 ASP cc_start: 0.8804 (m-30) cc_final: 0.7877 (t0) REVERT: G 213 ASP cc_start: 0.8742 (t0) cc_final: 0.8482 (t0) REVERT: G 228 GLN cc_start: 0.8453 (tt0) cc_final: 0.7883 (tm-30) REVERT: G 230 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7647 (mt-10) REVERT: G 261 LEU cc_start: 0.7934 (pt) cc_final: 0.7646 (pt) REVERT: G 263 TRP cc_start: 0.8184 (m100) cc_final: 0.7829 (m100) REVERT: G 269 ASN cc_start: 0.7920 (m-40) cc_final: 0.7299 (m-40) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.2915 time to fit residues: 194.7179 Evaluate side-chains 420 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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: 0.0870 chunk 32 optimal weight: 0.4980 chunk 139 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 147 optimal weight: 0.0770 chunk 26 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN B 273 GLN C 54 HIS C 228 GLN D 117 GLN D 135 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 273 GLN G 135 HIS G 146 HIS G 228 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.087900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.072761 restraints weight = 45763.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.075820 restraints weight = 25573.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.077963 restraints weight = 16643.166| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.446 16952 Z= 0.168 Angle : 0.853 11.974 23765 Z= 0.334 Chirality : 0.047 0.142 2128 Planarity : 0.005 0.036 2912 Dihedral : 17.860 89.348 2303 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -2.10 (0.20), residues: 1792 helix: -1.91 (0.26), residues: 294 sheet: None (None), residues: 0 loop : -1.41 (0.17), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 279 HIS 0.006 0.001 HIS G 276 PHE 0.021 0.002 PHE F 108 TYR 0.014 0.002 TYR B 133 ARG 0.004 0.001 ARG E 197 Details of bonding type rmsd hydrogen bonds : bond 0.02794 ( 154) hydrogen bonds : angle 6.82587 ( 441) covalent geometry : bond 0.00472 (16772) covalent geometry : angle 0.85287 (23765) Misc. bond : bond 0.11966 ( 180) =============================================================================== Job complete usr+sys time: 5633.02 seconds wall clock time: 99 minutes 43.25 seconds (5983.25 seconds total)