Starting phenix.real_space_refine on Tue Dec 31 14:17:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d9m_27266/12_2024/8d9m_27266.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d9m_27266/12_2024/8d9m_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_27266/12_2024/8d9m_27266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d9m_27266/12_2024/8d9m_27266.map" model { file = "/net/cci-nas-00/data/ceres_data/8d9m_27266/12_2024/8d9m_27266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d9m_27266/12_2024/8d9m_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-5532/modules/chem_data/mon_lib" Total number of atoms: 15967 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1937 Classifications: {'peptide': 258} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 236} Chain: "A" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 344 Unusual residues: {'HEC': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 6.43, per 1000 atoms: 0.40 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: 5.04 Conformation dependent library (CDL) restraints added in 1.8 seconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3318 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 14 sheets defined 19.4% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 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: 3.59 Time building geometry restraints manager: 5.50 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 32.080 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.380 ------------------------------------------------------------------------------- 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 : 0.007 0.098 16772 Z= 0.429 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 *********************** 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 : 1.562 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: 0.3152 time to fit residues: 185.5974 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 : 1.680 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.9990 chunk 83 optimal weight: 0.2980 chunk 102 optimal weight: 0.4980 chunk 158 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 G 146 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 16772 Z= 0.295 Angle : 0.904 12.040 23765 Z= 0.339 Chirality : 0.047 0.140 2128 Planarity : 0.006 0.070 2912 Dihedral : 17.754 89.681 2303 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 4.08 % 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: -2.39 (0.19), residues: 1792 helix: -1.40 (0.28), residues: 287 sheet: -1.21 (0.33), residues: 154 loop : -1.81 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 279 HIS 0.007 0.001 HIS B 64 PHE 0.013 0.001 PHE B 103 TYR 0.012 0.002 TYR E 133 ARG 0.001 0.000 ARG G 197 *********************** 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 437 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 1.578 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 61 VAL cc_start: 0.9201 (m) cc_final: 0.8953 (p) REVERT: B 63 GLN cc_start: 0.8600 (mt0) cc_final: 0.8325 (mt0) REVERT: B 79 ASN cc_start: 0.7953 (t0) cc_final: 0.7480 (t0) REVERT: B 95 MET cc_start: 0.8513 (mmm) cc_final: 0.8244 (mmm) REVERT: B 129 LYS cc_start: 0.9366 (ptpp) cc_final: 0.9081 (mttp) REVERT: B 203 GLN cc_start: 0.9012 (tp40) cc_final: 0.8369 (tp40) REVERT: B 204 ASP cc_start: 0.8862 (m-30) cc_final: 0.8474 (m-30) REVERT: B 230 GLU cc_start: 0.8216 (mt-10) cc_final: 0.8012 (mt-10) REVERT: B 269 ASN cc_start: 0.8075 (m-40) cc_final: 0.7402 (t0) REVERT: C 51 LEU cc_start: 0.7489 (mt) cc_final: 0.7284 (mt) REVERT: C 79 ASN cc_start: 0.7791 (t0) cc_final: 0.7236 (t0) REVERT: C 95 MET cc_start: 0.8630 (mmm) cc_final: 0.8251 (mmm) REVERT: C 108 PHE cc_start: 0.8827 (p90) cc_final: 0.8392 (p90) REVERT: C 116 THR cc_start: 0.8869 (m) cc_final: 0.8329 (t) REVERT: C 117 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8053 (mm-40) REVERT: C 179 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7423 (mt-10) REVERT: C 183 GLN cc_start: 0.4737 (pm20) cc_final: 0.4393 (pm20) REVERT: C 203 GLN cc_start: 0.8970 (tp40) cc_final: 0.8282 (tp40) REVERT: C 204 ASP cc_start: 0.8720 (m-30) cc_final: 0.8393 (m-30) REVERT: C 263 TRP cc_start: 0.8304 (m100) cc_final: 0.7433 (m100) REVERT: C 269 ASN cc_start: 0.7553 (m-40) cc_final: 0.6864 (t0) REVERT: C 279 TRP cc_start: 0.7641 (t-100) cc_final: 0.7257 (t-100) REVERT: D 37 ILE cc_start: 0.8625 (pt) cc_final: 0.8309 (pt) REVERT: D 79 ASN cc_start: 0.7878 (t0) cc_final: 0.7480 (t0) REVERT: D 176 GLN cc_start: 0.7172 (tm-30) cc_final: 0.6960 (tm-30) REVERT: D 203 GLN cc_start: 0.9042 (tp40) cc_final: 0.8440 (tp40) REVERT: D 204 ASP cc_start: 0.8802 (m-30) cc_final: 0.8493 (m-30) REVERT: D 226 ILE cc_start: 0.9003 (tp) cc_final: 0.8780 (tp) REVERT: D 227 ARG cc_start: 0.8809 (mmt180) cc_final: 0.8436 (mtt180) REVERT: D 230 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7658 (mt-10) REVERT: D 242 GLN cc_start: 0.8157 (tp40) cc_final: 0.7883 (tp-100) REVERT: D 269 ASN cc_start: 0.7741 (m-40) cc_final: 0.7096 (t0) REVERT: D 273 GLN cc_start: 0.8483 (mt0) cc_final: 0.8136 (mt0) REVERT: A 37 ILE cc_start: 0.8562 (pt) cc_final: 0.8332 (pt) REVERT: A 61 VAL cc_start: 0.9254 (m) cc_final: 0.8996 (p) REVERT: A 146 HIS cc_start: 0.8135 (p-80) cc_final: 0.7926 (p90) REVERT: A 203 GLN cc_start: 0.9000 (tp40) cc_final: 0.8607 (tp40) REVERT: A 204 ASP cc_start: 0.8744 (m-30) cc_final: 0.8475 (m-30) REVERT: A 226 ILE cc_start: 0.8973 (tp) cc_final: 0.8580 (tp) REVERT: A 227 ARG cc_start: 0.8955 (mtt180) cc_final: 0.8325 (mmt180) REVERT: A 230 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7275 (mt-10) REVERT: A 269 ASN cc_start: 0.7602 (m-40) cc_final: 0.7275 (t0) REVERT: E 61 VAL cc_start: 0.9165 (m) cc_final: 0.8964 (p) REVERT: E 79 ASN cc_start: 0.8010 (t0) cc_final: 0.7393 (t0) REVERT: E 129 LYS cc_start: 0.9187 (ptpp) cc_final: 0.8926 (mttp) REVERT: E 133 TYR cc_start: 0.8703 (t80) cc_final: 0.8467 (t80) REVERT: E 176 GLN cc_start: 0.7503 (tm-30) cc_final: 0.7131 (tm-30) REVERT: E 203 GLN cc_start: 0.8949 (tp40) cc_final: 0.8599 (tp40) REVERT: E 204 ASP cc_start: 0.8596 (m-30) cc_final: 0.8322 (m-30) REVERT: E 216 LEU cc_start: 0.8893 (tt) cc_final: 0.8285 (mt) REVERT: E 273 GLN cc_start: 0.8671 (mt0) cc_final: 0.8398 (mt0) REVERT: F 79 ASN cc_start: 0.7909 (t0) cc_final: 0.7534 (t0) REVERT: F 95 MET cc_start: 0.8648 (mmm) cc_final: 0.8434 (mmp) REVERT: F 108 PHE cc_start: 0.8908 (p90) cc_final: 0.8265 (p90) REVERT: F 176 GLN cc_start: 0.7559 (tm-30) cc_final: 0.7258 (tm-30) REVERT: F 203 GLN cc_start: 0.8971 (tp40) cc_final: 0.8652 (tp40) REVERT: F 204 ASP cc_start: 0.8856 (m-30) cc_final: 0.8409 (m-30) REVERT: F 226 ILE cc_start: 0.8985 (tp) cc_final: 0.8637 (tp) REVERT: F 227 ARG cc_start: 0.8772 (mmt180) cc_final: 0.8336 (mtt180) REVERT: F 230 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7415 (mt-10) REVERT: F 269 ASN cc_start: 0.7725 (m-40) cc_final: 0.7339 (t0) REVERT: G 37 ILE cc_start: 0.8462 (pt) cc_final: 0.8159 (pt) REVERT: G 42 PHE cc_start: 0.8012 (t80) cc_final: 0.7769 (t80) REVERT: G 79 ASN cc_start: 0.7871 (t0) cc_final: 0.7636 (t0) REVERT: G 129 LYS cc_start: 0.9408 (ptpp) cc_final: 0.9041 (mttt) REVERT: G 140 ASP cc_start: 0.8372 (m-30) cc_final: 0.7918 (t0) REVERT: G 141 ASN cc_start: 0.8836 (t0) cc_final: 0.8432 (t0) REVERT: G 179 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7391 (mt-10) REVERT: G 182 HIS cc_start: 0.8403 (m-70) cc_final: 0.7673 (m170) REVERT: G 183 GLN cc_start: 0.5013 (pm20) cc_final: 0.4601 (pm20) REVERT: G 203 GLN cc_start: 0.9100 (tp40) cc_final: 0.8323 (tp40) REVERT: G 204 ASP cc_start: 0.8917 (m-30) cc_final: 0.8488 (m-30) REVERT: G 226 ILE cc_start: 0.8905 (tp) cc_final: 0.8611 (tp) REVERT: G 227 ARG cc_start: 0.8742 (mmt180) cc_final: 0.8117 (mtt180) REVERT: G 230 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7718 (mt-10) REVERT: G 238 LEU cc_start: 0.8879 (mt) cc_final: 0.8679 (mt) REVERT: G 241 ILE cc_start: 0.9004 (pt) cc_final: 0.8780 (pt) REVERT: G 242 GLN cc_start: 0.8150 (tp40) cc_final: 0.7799 (tp-100) REVERT: G 269 ASN cc_start: 0.7500 (m-40) cc_final: 0.6950 (t0) REVERT: G 279 TRP cc_start: 0.7588 (t-100) cc_final: 0.7265 (t-100) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.3067 time to fit residues: 191.4877 Evaluate side-chains 395 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.0970 chunk 132 optimal weight: 0.8980 chunk 108 optimal weight: 0.0570 chunk 43 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 157 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN C 63 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 HIS ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN A 135 HIS A 228 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN E 135 HIS ** E 146 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 273 GLN ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 16772 Z= 0.292 Angle : 0.848 10.351 23765 Z= 0.332 Chirality : 0.048 0.150 2128 Planarity : 0.005 0.057 2912 Dihedral : 17.795 89.784 2303 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.39 % Favored : 87.61 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.20), residues: 1792 helix: -1.38 (0.29), residues: 287 sheet: -0.76 (0.51), residues: 70 loop : -1.45 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 279 HIS 0.007 0.001 HIS G 276 PHE 0.013 0.001 PHE A 103 TYR 0.014 0.002 TYR A 133 ARG 0.006 0.001 ARG C 109 *********************** 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 439 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 LEU cc_start: 0.7498 (mt) cc_final: 0.7293 (mt) REVERT: B 61 VAL cc_start: 0.9202 (m) cc_final: 0.8937 (p) REVERT: B 63 GLN cc_start: 0.8636 (mt0) cc_final: 0.8315 (mt0) REVERT: B 79 ASN cc_start: 0.7904 (t0) cc_final: 0.7460 (t0) REVERT: B 95 MET cc_start: 0.8482 (mmm) cc_final: 0.8240 (mmm) REVERT: B 129 LYS cc_start: 0.9345 (ptpp) cc_final: 0.9054 (mttp) REVERT: B 146 HIS cc_start: 0.8267 (p90) cc_final: 0.7892 (p90) REVERT: B 203 GLN cc_start: 0.9029 (tp40) cc_final: 0.8351 (tp40) REVERT: B 204 ASP cc_start: 0.8802 (m-30) cc_final: 0.8382 (m-30) REVERT: B 269 ASN cc_start: 0.7867 (m-40) cc_final: 0.7284 (t0) REVERT: C 62 GLN cc_start: 0.8539 (mm110) cc_final: 0.8292 (mm110) REVERT: C 79 ASN cc_start: 0.7756 (t0) cc_final: 0.7152 (t0) REVERT: C 116 THR cc_start: 0.8827 (m) cc_final: 0.8330 (t) REVERT: C 117 GLN cc_start: 0.8309 (mm-40) cc_final: 0.8028 (mm-40) REVERT: C 129 LYS cc_start: 0.9250 (ptpp) cc_final: 0.9036 (mttp) REVERT: C 141 ASN cc_start: 0.8788 (t0) cc_final: 0.8422 (t0) REVERT: C 179 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7386 (mt-10) REVERT: C 183 GLN cc_start: 0.6585 (pm20) cc_final: 0.5916 (pm20) REVERT: C 203 GLN cc_start: 0.8960 (tp40) cc_final: 0.8259 (tp40) REVERT: C 204 ASP cc_start: 0.8671 (m-30) cc_final: 0.8374 (m-30) REVERT: C 261 LEU cc_start: 0.7984 (pt) cc_final: 0.7783 (pt) REVERT: C 263 TRP cc_start: 0.8313 (m100) cc_final: 0.7595 (m100) REVERT: C 279 TRP cc_start: 0.7643 (t-100) cc_final: 0.7427 (t-100) REVERT: D 51 LEU cc_start: 0.7344 (mt) cc_final: 0.7138 (mt) REVERT: D 79 ASN cc_start: 0.7901 (t0) cc_final: 0.7476 (t0) REVERT: D 108 PHE cc_start: 0.8736 (p90) cc_final: 0.8292 (p90) REVERT: D 203 GLN cc_start: 0.9054 (tp40) cc_final: 0.8494 (tp40) REVERT: D 204 ASP cc_start: 0.8783 (m-30) cc_final: 0.8419 (m-30) REVERT: D 226 ILE cc_start: 0.9013 (tp) cc_final: 0.8698 (tp) REVERT: D 230 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7592 (mt-10) REVERT: D 242 GLN cc_start: 0.8214 (tp40) cc_final: 0.7899 (tp-100) REVERT: D 269 ASN cc_start: 0.7741 (m-40) cc_final: 0.7162 (m-40) REVERT: A 37 ILE cc_start: 0.8431 (pt) cc_final: 0.8158 (pt) REVERT: A 129 LYS cc_start: 0.9335 (ptpp) cc_final: 0.8979 (mttm) REVERT: A 141 ASN cc_start: 0.8755 (t0) cc_final: 0.8322 (t0) REVERT: A 144 ASP cc_start: 0.7907 (p0) cc_final: 0.7594 (p0) REVERT: A 146 HIS cc_start: 0.8119 (p-80) cc_final: 0.7837 (p90) REVERT: A 176 GLN cc_start: 0.7577 (tm-30) cc_final: 0.7092 (tm-30) REVERT: A 203 GLN cc_start: 0.8984 (tp40) cc_final: 0.8626 (tp40) REVERT: A 204 ASP cc_start: 0.8726 (m-30) cc_final: 0.8425 (m-30) REVERT: A 226 ILE cc_start: 0.8990 (tp) cc_final: 0.8701 (tp) REVERT: A 230 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7253 (mt-10) REVERT: A 269 ASN cc_start: 0.7591 (m-40) cc_final: 0.7044 (m-40) REVERT: E 61 VAL cc_start: 0.9241 (m) cc_final: 0.8988 (p) REVERT: E 63 GLN cc_start: 0.8674 (mt0) cc_final: 0.8423 (mt0) REVERT: E 79 ASN cc_start: 0.7960 (t0) cc_final: 0.7407 (t0) REVERT: E 129 LYS cc_start: 0.9169 (ptpp) cc_final: 0.8967 (mttp) REVERT: E 133 TYR cc_start: 0.8661 (t80) cc_final: 0.8394 (t80) REVERT: E 135 HIS cc_start: 0.7175 (p90) cc_final: 0.6784 (p-80) REVERT: E 146 HIS cc_start: 0.8340 (p90) cc_final: 0.7761 (p90) REVERT: E 148 ILE cc_start: 0.9256 (mm) cc_final: 0.8740 (mm) REVERT: E 203 GLN cc_start: 0.8932 (tp40) cc_final: 0.8550 (tp40) REVERT: E 204 ASP cc_start: 0.8569 (m-30) cc_final: 0.8255 (m-30) REVERT: E 269 ASN cc_start: 0.7793 (m-40) cc_final: 0.6823 (m-40) REVERT: E 273 GLN cc_start: 0.8649 (mt0) cc_final: 0.8310 (mt0) REVERT: F 79 ASN cc_start: 0.7832 (t0) cc_final: 0.7417 (t0) REVERT: F 95 MET cc_start: 0.8533 (mmm) cc_final: 0.8305 (mmp) REVERT: F 108 PHE cc_start: 0.8788 (p90) cc_final: 0.8529 (p90) REVERT: F 109 ARG cc_start: 0.8782 (mmt180) cc_final: 0.8484 (mmt180) REVERT: F 116 THR cc_start: 0.8919 (t) cc_final: 0.8683 (t) REVERT: F 203 GLN cc_start: 0.8959 (tp40) cc_final: 0.8631 (tp40) REVERT: F 204 ASP cc_start: 0.8826 (m-30) cc_final: 0.8352 (m-30) REVERT: F 226 ILE cc_start: 0.8975 (tp) cc_final: 0.8606 (tp) REVERT: F 228 GLN cc_start: 0.8751 (tt0) cc_final: 0.8284 (tm-30) REVERT: F 230 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7520 (mt-10) REVERT: F 269 ASN cc_start: 0.7613 (m-40) cc_final: 0.6961 (m-40) REVERT: G 37 ILE cc_start: 0.8550 (pt) cc_final: 0.8227 (pt) REVERT: G 79 ASN cc_start: 0.7966 (t0) cc_final: 0.7555 (t0) REVERT: G 116 THR cc_start: 0.8777 (t) cc_final: 0.8299 (t) REVERT: G 117 GLN cc_start: 0.8305 (mm110) cc_final: 0.8091 (mm110) REVERT: G 129 LYS cc_start: 0.9336 (ptpp) cc_final: 0.9035 (mttt) REVERT: G 135 HIS cc_start: 0.7426 (p-80) cc_final: 0.7086 (p-80) REVERT: G 141 ASN cc_start: 0.8811 (t0) cc_final: 0.8508 (t0) REVERT: G 179 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7215 (mt-10) REVERT: G 182 HIS cc_start: 0.8404 (m-70) cc_final: 0.7628 (m-70) REVERT: G 203 GLN cc_start: 0.9091 (tp40) cc_final: 0.8287 (tp40) REVERT: G 204 ASP cc_start: 0.8841 (m-30) cc_final: 0.8438 (m-30) REVERT: G 231 VAL cc_start: 0.8653 (t) cc_final: 0.8396 (p) REVERT: G 238 LEU cc_start: 0.8939 (mt) cc_final: 0.8658 (mp) REVERT: G 269 ASN cc_start: 0.7432 (m-40) cc_final: 0.6889 (m-40) REVERT: G 279 TRP cc_start: 0.7576 (t-100) cc_final: 0.7207 (t-100) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.3155 time to fit residues: 198.9762 Evaluate side-chains 393 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.0770 chunk 119 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 169 optimal weight: 0.0040 chunk 83 optimal weight: 0.6980 chunk 151 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.3350 ------------------------------------------------------------------------------- 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** B 273 GLN C 228 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN D 117 GLN D 146 HIS D 228 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 HIS F 228 GLN F 273 GLN G 63 GLN G 146 HIS G 228 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16772 Z= 0.251 Angle : 0.824 10.017 23765 Z= 0.324 Chirality : 0.046 0.137 2128 Planarity : 0.005 0.050 2912 Dihedral : 17.759 88.931 2303 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.20), residues: 1792 helix: -1.60 (0.26), residues: 301 sheet: -1.01 (0.53), residues: 70 loop : -1.36 (0.18), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 279 HIS 0.006 0.001 HIS A 65 PHE 0.018 0.001 PHE C 108 TYR 0.017 0.002 TYR D 133 ARG 0.002 0.000 ARG E 197 *********************** 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 440 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7356 (mt) cc_final: 0.7141 (mt) REVERT: B 61 VAL cc_start: 0.9171 (m) cc_final: 0.8912 (p) REVERT: B 63 GLN cc_start: 0.8559 (mt0) cc_final: 0.8266 (mt0) REVERT: B 79 ASN cc_start: 0.7866 (t0) cc_final: 0.7386 (t0) REVERT: B 95 MET cc_start: 0.8715 (mmm) cc_final: 0.8440 (mmp) REVERT: B 112 PHE cc_start: 0.7359 (m-80) cc_final: 0.7114 (m-80) REVERT: B 129 LYS cc_start: 0.9299 (ptpp) cc_final: 0.9039 (mttp) REVERT: B 135 HIS cc_start: 0.7088 (p90) cc_final: 0.6830 (p-80) REVERT: B 146 HIS cc_start: 0.8206 (p90) cc_final: 0.7972 (p-80) REVERT: B 203 GLN cc_start: 0.9048 (tp40) cc_final: 0.8775 (tp40) REVERT: B 204 ASP cc_start: 0.8724 (m-30) cc_final: 0.8329 (m-30) REVERT: B 227 ARG cc_start: 0.9114 (mtt180) cc_final: 0.8822 (mmm160) REVERT: B 228 GLN cc_start: 0.8511 (tt0) cc_final: 0.7942 (tm-30) REVERT: B 263 TRP cc_start: 0.8232 (m100) cc_final: 0.7570 (m100) REVERT: C 51 LEU cc_start: 0.7095 (mt) cc_final: 0.6888 (mt) REVERT: C 79 ASN cc_start: 0.7736 (t0) cc_final: 0.7322 (t0) REVERT: C 90 THR cc_start: 0.8546 (p) cc_final: 0.8255 (t) REVERT: C 95 MET cc_start: 0.8667 (mmp) cc_final: 0.8457 (mmp) REVERT: C 109 ARG cc_start: 0.8814 (mmt180) cc_final: 0.8398 (tpp-160) REVERT: C 116 THR cc_start: 0.8814 (m) cc_final: 0.8311 (t) REVERT: C 117 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7920 (mm110) REVERT: C 135 HIS cc_start: 0.7168 (p90) cc_final: 0.6931 (p90) REVERT: C 179 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7033 (mt-10) REVERT: C 183 GLN cc_start: 0.6105 (pm20) cc_final: 0.5496 (pm20) REVERT: C 203 GLN cc_start: 0.8988 (tp40) cc_final: 0.8158 (tp40) REVERT: C 204 ASP cc_start: 0.8639 (m-30) cc_final: 0.8315 (m-30) REVERT: C 263 TRP cc_start: 0.8265 (m100) cc_final: 0.7629 (m100) REVERT: C 269 ASN cc_start: 0.7453 (m-40) cc_final: 0.6979 (m-40) REVERT: C 279 TRP cc_start: 0.7595 (t-100) cc_final: 0.7350 (t-100) REVERT: D 51 LEU cc_start: 0.7273 (mt) cc_final: 0.7060 (mt) REVERT: D 79 ASN cc_start: 0.7880 (t0) cc_final: 0.7463 (t0) REVERT: D 108 PHE cc_start: 0.8737 (p90) cc_final: 0.7781 (p90) REVERT: D 141 ASN cc_start: 0.8854 (t0) cc_final: 0.8519 (t0) REVERT: D 203 GLN cc_start: 0.9041 (tp40) cc_final: 0.8480 (tp40) REVERT: D 204 ASP cc_start: 0.8714 (m-30) cc_final: 0.8347 (m-30) REVERT: D 213 ASP cc_start: 0.8525 (t0) cc_final: 0.8295 (t0) REVERT: D 226 ILE cc_start: 0.9078 (tp) cc_final: 0.8852 (tp) REVERT: D 227 ARG cc_start: 0.8593 (mmt90) cc_final: 0.8030 (mtt180) REVERT: D 230 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7521 (mt-10) REVERT: A 37 ILE cc_start: 0.8410 (pt) cc_final: 0.8065 (pt) REVERT: A 108 PHE cc_start: 0.8775 (p90) cc_final: 0.8569 (p90) REVERT: A 129 LYS cc_start: 0.9321 (ptpp) cc_final: 0.8967 (mtmm) REVERT: A 133 TYR cc_start: 0.8567 (t80) cc_final: 0.8356 (t80) REVERT: A 135 HIS cc_start: 0.7444 (p-80) cc_final: 0.7151 (p-80) REVERT: A 176 GLN cc_start: 0.7491 (tm-30) cc_final: 0.7252 (tm-30) REVERT: A 203 GLN cc_start: 0.8945 (tp40) cc_final: 0.8573 (tp40) REVERT: A 227 ARG cc_start: 0.8702 (mtt180) cc_final: 0.8003 (mmt90) REVERT: A 230 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7029 (mt-10) REVERT: A 260 ASP cc_start: 0.7769 (t0) cc_final: 0.7555 (t0) REVERT: A 261 LEU cc_start: 0.8137 (pt) cc_final: 0.7850 (pt) REVERT: A 269 ASN cc_start: 0.7413 (m-40) cc_final: 0.6879 (m-40) REVERT: E 63 GLN cc_start: 0.8696 (mt0) cc_final: 0.8360 (mp10) REVERT: E 79 ASN cc_start: 0.7960 (t0) cc_final: 0.7354 (t0) REVERT: E 133 TYR cc_start: 0.8681 (t80) cc_final: 0.8382 (t80) REVERT: E 176 GLN cc_start: 0.7512 (tm-30) cc_final: 0.7259 (tm-30) REVERT: E 203 GLN cc_start: 0.8987 (tp40) cc_final: 0.8547 (tp40) REVERT: E 204 ASP cc_start: 0.8586 (m-30) cc_final: 0.8239 (m-30) REVERT: E 260 ASP cc_start: 0.7901 (t0) cc_final: 0.7591 (t0) REVERT: E 261 LEU cc_start: 0.8142 (pt) cc_final: 0.7838 (pt) REVERT: E 269 ASN cc_start: 0.7738 (m-40) cc_final: 0.6881 (m-40) REVERT: F 79 ASN cc_start: 0.7823 (t0) cc_final: 0.7424 (t0) REVERT: F 95 MET cc_start: 0.8685 (mmm) cc_final: 0.8327 (mmm) REVERT: F 108 PHE cc_start: 0.8764 (p90) cc_final: 0.8533 (p90) REVERT: F 116 THR cc_start: 0.8856 (t) cc_final: 0.8623 (t) REVERT: F 129 LYS cc_start: 0.9263 (mttp) cc_final: 0.8706 (tppt) REVERT: F 135 HIS cc_start: 0.7121 (p90) cc_final: 0.6587 (p90) REVERT: F 176 GLN cc_start: 0.7500 (tm-30) cc_final: 0.7245 (tm-30) REVERT: F 203 GLN cc_start: 0.8992 (tp40) cc_final: 0.8693 (tp40) REVERT: F 204 ASP cc_start: 0.8786 (m-30) cc_final: 0.8358 (m-30) REVERT: F 216 LEU cc_start: 0.8945 (tt) cc_final: 0.8140 (mt) REVERT: F 226 ILE cc_start: 0.9014 (tp) cc_final: 0.8737 (tp) REVERT: F 227 ARG cc_start: 0.8583 (mmt180) cc_final: 0.8361 (mtt180) REVERT: F 230 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7580 (mt-10) REVERT: F 243 LYS cc_start: 0.8774 (tmtt) cc_final: 0.8378 (tptp) REVERT: F 263 TRP cc_start: 0.8358 (m100) cc_final: 0.7773 (m100) REVERT: F 269 ASN cc_start: 0.8127 (m-40) cc_final: 0.7277 (m-40) REVERT: G 37 ILE cc_start: 0.8462 (pt) cc_final: 0.8139 (pt) REVERT: G 79 ASN cc_start: 0.8003 (t0) cc_final: 0.7605 (t0) REVERT: G 116 THR cc_start: 0.8723 (t) cc_final: 0.8214 (t) REVERT: G 117 GLN cc_start: 0.8282 (mm110) cc_final: 0.8062 (mm110) REVERT: G 129 LYS cc_start: 0.9342 (ptpp) cc_final: 0.8981 (mttp) REVERT: G 135 HIS cc_start: 0.7513 (p-80) cc_final: 0.7010 (p-80) REVERT: G 203 GLN cc_start: 0.9112 (tp40) cc_final: 0.8245 (tp40) REVERT: G 204 ASP cc_start: 0.8807 (m-30) cc_final: 0.8449 (m-30) REVERT: G 226 ILE cc_start: 0.8960 (tp) cc_final: 0.8732 (tp) REVERT: G 227 ARG cc_start: 0.8555 (mmt90) cc_final: 0.7782 (mmt90) REVERT: G 228 GLN cc_start: 0.8476 (tt0) cc_final: 0.8030 (tm-30) REVERT: G 230 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7472 (mt-10) REVERT: G 269 ASN cc_start: 0.7368 (m-40) cc_final: 0.6820 (m-40) outliers start: 0 outliers final: 0 residues processed: 440 average time/residue: 0.3140 time to fit residues: 202.4866 Evaluate side-chains 389 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 0.0570 chunk 144 optimal weight: 5.9990 chunk 116 optimal weight: 0.0020 chunk 0 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.7510 ------------------------------------------------------------------------------- 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** B 273 GLN ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN D 228 GLN D 273 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN A 146 HIS A 228 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN E 135 HIS E 228 GLN E 273 GLN F 63 GLN ** F 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 273 GLN G 146 HIS G 228 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 16772 Z= 0.350 Angle : 0.882 11.147 23765 Z= 0.340 Chirality : 0.048 0.141 2128 Planarity : 0.005 0.044 2912 Dihedral : 17.959 89.643 2303 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.56 % Favored : 86.44 % Rotamer: Outliers : 0.06 % Allowed : 2.38 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.20), residues: 1792 helix: -1.62 (0.26), residues: 294 sheet: -1.47 (0.56), residues: 70 loop : -1.38 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 279 HIS 0.007 0.001 HIS D 276 PHE 0.016 0.002 PHE D 103 TYR 0.015 0.002 TYR B 133 ARG 0.006 0.000 ARG E 197 *********************** 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 443 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 442 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 THR cc_start: 0.8269 (t) cc_final: 0.7822 (p) REVERT: B 51 LEU cc_start: 0.7530 (mt) cc_final: 0.7319 (mt) REVERT: B 63 GLN cc_start: 0.8704 (mt0) cc_final: 0.8404 (mt0) REVERT: B 79 ASN cc_start: 0.7973 (t0) cc_final: 0.7574 (t0) REVERT: B 95 MET cc_start: 0.8754 (mmm) cc_final: 0.8394 (mmm) REVERT: B 129 LYS cc_start: 0.9287 (ptpp) cc_final: 0.9041 (mttp) REVERT: B 183 GLN cc_start: 0.7390 (pm20) cc_final: 0.7141 (pm20) REVERT: B 203 GLN cc_start: 0.9064 (tp40) cc_final: 0.8724 (tp40) REVERT: B 204 ASP cc_start: 0.8820 (m-30) cc_final: 0.8412 (m-30) REVERT: C 46 THR cc_start: 0.8077 (t) cc_final: 0.7533 (p) REVERT: C 51 LEU cc_start: 0.7326 (mt) cc_final: 0.7117 (mt) REVERT: C 79 ASN cc_start: 0.7913 (t0) cc_final: 0.7559 (t0) REVERT: C 90 THR cc_start: 0.8571 (p) cc_final: 0.8293 (t) REVERT: C 95 MET cc_start: 0.8715 (mmp) cc_final: 0.8466 (mmp) REVERT: C 116 THR cc_start: 0.8765 (m) cc_final: 0.8312 (t) REVERT: C 129 LYS cc_start: 0.9297 (mttp) cc_final: 0.9050 (mmtm) REVERT: C 135 HIS cc_start: 0.7329 (p90) cc_final: 0.6895 (p-80) REVERT: C 179 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7369 (mt-10) REVERT: C 182 HIS cc_start: 0.8261 (m-70) cc_final: 0.7534 (m170) REVERT: C 183 GLN cc_start: 0.5919 (pm20) cc_final: 0.5664 (pm20) REVERT: C 203 GLN cc_start: 0.9036 (tp40) cc_final: 0.7858 (tp40) REVERT: C 204 ASP cc_start: 0.8710 (m-30) cc_final: 0.8371 (m-30) REVERT: C 243 LYS cc_start: 0.8754 (tmtt) cc_final: 0.8370 (tptp) REVERT: C 263 TRP cc_start: 0.8318 (m100) cc_final: 0.7770 (m100) REVERT: C 269 ASN cc_start: 0.7517 (m-40) cc_final: 0.6929 (m-40) REVERT: C 279 TRP cc_start: 0.7713 (t-100) cc_final: 0.7461 (t-100) REVERT: D 51 LEU cc_start: 0.7494 (mt) cc_final: 0.7262 (mt) REVERT: D 79 ASN cc_start: 0.7914 (t0) cc_final: 0.7568 (t0) REVERT: D 108 PHE cc_start: 0.8804 (p90) cc_final: 0.7966 (p90) REVERT: D 109 ARG cc_start: 0.9062 (mmt180) cc_final: 0.8737 (mmt180) REVERT: D 129 LYS cc_start: 0.9316 (mttp) cc_final: 0.9056 (mmtm) REVERT: D 203 GLN cc_start: 0.9064 (tp40) cc_final: 0.8416 (tp40) REVERT: D 204 ASP cc_start: 0.8840 (m-30) cc_final: 0.8463 (m-30) REVERT: D 226 ILE cc_start: 0.9049 (tp) cc_final: 0.8830 (tp) REVERT: D 227 ARG cc_start: 0.8587 (mmt90) cc_final: 0.8046 (mtt180) REVERT: D 228 GLN cc_start: 0.8350 (tt0) cc_final: 0.7873 (tm-30) REVERT: D 230 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7684 (mt-10) REVERT: D 238 LEU cc_start: 0.8978 (mt) cc_final: 0.8763 (mt) REVERT: D 242 GLN cc_start: 0.8127 (tp40) cc_final: 0.7847 (tp-100) REVERT: D 269 ASN cc_start: 0.7660 (m-40) cc_final: 0.7163 (m-40) REVERT: D 279 TRP cc_start: 0.7890 (t60) cc_final: 0.7628 (t-100) REVERT: A 34 PHE cc_start: 0.8673 (p90) cc_final: 0.8472 (p90) REVERT: A 51 LEU cc_start: 0.7533 (mt) cc_final: 0.7329 (mt) REVERT: A 129 LYS cc_start: 0.9312 (ptpp) cc_final: 0.8981 (mtmm) REVERT: A 133 TYR cc_start: 0.8628 (t80) cc_final: 0.8352 (t80) REVERT: A 135 HIS cc_start: 0.7688 (p-80) cc_final: 0.7299 (p-80) REVERT: A 140 ASP cc_start: 0.7922 (t0) cc_final: 0.7644 (t0) REVERT: A 141 ASN cc_start: 0.8804 (t0) cc_final: 0.8574 (t0) REVERT: A 176 GLN cc_start: 0.7563 (tm-30) cc_final: 0.7274 (tm-30) REVERT: A 203 GLN cc_start: 0.9024 (tp40) cc_final: 0.8563 (tp40) REVERT: A 204 ASP cc_start: 0.8839 (m-30) cc_final: 0.8541 (m-30) REVERT: A 227 ARG cc_start: 0.8741 (mtt180) cc_final: 0.8265 (mtt180) REVERT: A 230 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7261 (mt-10) REVERT: A 255 LYS cc_start: 0.8758 (pttm) cc_final: 0.8539 (ptpp) REVERT: A 260 ASP cc_start: 0.7914 (t0) cc_final: 0.7575 (t0) REVERT: A 261 LEU cc_start: 0.8249 (pt) cc_final: 0.7907 (pt) REVERT: A 269 ASN cc_start: 0.7525 (m-40) cc_final: 0.7079 (m-40) REVERT: E 51 LEU cc_start: 0.7647 (mt) cc_final: 0.7414 (mt) REVERT: E 63 GLN cc_start: 0.8767 (mt0) cc_final: 0.8374 (mt0) REVERT: E 79 ASN cc_start: 0.8058 (t0) cc_final: 0.7543 (t0) REVERT: E 108 PHE cc_start: 0.8861 (p90) cc_final: 0.8559 (p90) REVERT: E 133 TYR cc_start: 0.8728 (t80) cc_final: 0.8437 (t80) REVERT: E 135 HIS cc_start: 0.7428 (p90) cc_final: 0.6930 (p-80) REVERT: E 146 HIS cc_start: 0.8142 (p90) cc_final: 0.7839 (p-80) REVERT: E 176 GLN cc_start: 0.7612 (tm-30) cc_final: 0.7335 (tm-30) REVERT: E 203 GLN cc_start: 0.9071 (tp40) cc_final: 0.8442 (tp40) REVERT: E 204 ASP cc_start: 0.8676 (m-30) cc_final: 0.8373 (m-30) REVERT: E 228 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.6929 (tm-30) REVERT: E 230 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7289 (tm-30) REVERT: E 269 ASN cc_start: 0.7580 (m-40) cc_final: 0.7073 (m-40) REVERT: F 46 THR cc_start: 0.8241 (t) cc_final: 0.7958 (p) REVERT: F 51 LEU cc_start: 0.7600 (mt) cc_final: 0.7381 (mt) REVERT: F 79 ASN cc_start: 0.7865 (t0) cc_final: 0.7460 (t0) REVERT: F 108 PHE cc_start: 0.8922 (p90) cc_final: 0.8626 (p90) REVERT: F 129 LYS cc_start: 0.9235 (mttp) cc_final: 0.8955 (tppt) REVERT: F 130 ASP cc_start: 0.7984 (t0) cc_final: 0.7777 (t0) REVERT: F 176 GLN cc_start: 0.7396 (tm-30) cc_final: 0.7135 (tm-30) REVERT: F 179 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7782 (mt-10) REVERT: F 203 GLN cc_start: 0.8997 (tp40) cc_final: 0.8162 (tp40) REVERT: F 204 ASP cc_start: 0.8888 (m-30) cc_final: 0.8409 (m-30) REVERT: F 226 ILE cc_start: 0.9015 (tp) cc_final: 0.8712 (tp) REVERT: F 227 ARG cc_start: 0.8360 (mmt90) cc_final: 0.8136 (mmt90) REVERT: F 228 GLN cc_start: 0.8525 (tt0) cc_final: 0.8099 (tm-30) REVERT: F 230 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7531 (mt-10) REVERT: F 243 LYS cc_start: 0.8876 (tmtt) cc_final: 0.8567 (tptp) REVERT: F 263 TRP cc_start: 0.8417 (m100) cc_final: 0.8058 (m100) REVERT: F 269 ASN cc_start: 0.7763 (m-40) cc_final: 0.7126 (m-40) REVERT: G 46 THR cc_start: 0.8252 (t) cc_final: 0.7745 (p) REVERT: G 79 ASN cc_start: 0.8151 (t0) cc_final: 0.7832 (t0) REVERT: G 116 THR cc_start: 0.8730 (t) cc_final: 0.8228 (t) REVERT: G 117 GLN cc_start: 0.8295 (mm110) cc_final: 0.8037 (mm110) REVERT: G 129 LYS cc_start: 0.9331 (ptpp) cc_final: 0.8988 (mttp) REVERT: G 135 HIS cc_start: 0.7654 (p-80) cc_final: 0.7203 (p-80) REVERT: G 141 ASN cc_start: 0.8924 (t0) cc_final: 0.8590 (t0) REVERT: G 179 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7301 (mt-10) REVERT: G 183 GLN cc_start: 0.5334 (pm20) cc_final: 0.4996 (pm20) REVERT: G 204 ASP cc_start: 0.8849 (m-30) cc_final: 0.8487 (m-30) REVERT: G 226 ILE cc_start: 0.8980 (tp) cc_final: 0.8752 (tp) REVERT: G 230 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7654 (mt-10) REVERT: G 263 TRP cc_start: 0.8290 (m100) cc_final: 0.7765 (m100) REVERT: G 269 ASN cc_start: 0.7514 (m-40) cc_final: 0.7012 (m-40) outliers start: 1 outliers final: 0 residues processed: 442 average time/residue: 0.2953 time to fit residues: 188.2151 Evaluate side-chains 414 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 413 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 0.0970 chunk 41 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 88 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 HIS B 228 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN A 146 HIS A 228 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN F 228 GLN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN G 146 HIS G 228 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 16772 Z= 0.294 Angle : 0.841 10.541 23765 Z= 0.329 Chirality : 0.047 0.138 2128 Planarity : 0.004 0.044 2912 Dihedral : 17.956 89.944 2303 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 1.36 % 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: -1.68 (0.26), residues: 294 sheet: -1.61 (0.58), residues: 70 loop : -1.42 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 279 HIS 0.007 0.001 HIS A 64 PHE 0.015 0.001 PHE C 108 TYR 0.018 0.002 TYR D 133 ARG 0.004 0.000 ARG E 197 *********************** 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 433 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 LEU cc_start: 0.7529 (mt) cc_final: 0.7311 (mt) REVERT: B 63 GLN cc_start: 0.8719 (mt0) cc_final: 0.8359 (mt0) REVERT: B 79 ASN cc_start: 0.7945 (t0) cc_final: 0.7558 (t0) REVERT: B 95 MET cc_start: 0.8731 (mmm) cc_final: 0.8433 (mmp) REVERT: B 135 HIS cc_start: 0.7476 (p90) cc_final: 0.7136 (p-80) REVERT: B 203 GLN cc_start: 0.9058 (tp40) cc_final: 0.8707 (tp40) REVERT: B 204 ASP cc_start: 0.8762 (m-30) cc_final: 0.8330 (m-30) REVERT: B 226 ILE cc_start: 0.9135 (tp) cc_final: 0.8879 (tp) REVERT: B 228 GLN cc_start: 0.8407 (tt0) cc_final: 0.7914 (tm-30) REVERT: B 255 LYS cc_start: 0.8824 (pttm) cc_final: 0.8601 (ptpp) REVERT: C 46 THR cc_start: 0.8093 (t) cc_final: 0.7580 (p) REVERT: C 51 LEU cc_start: 0.7170 (mt) cc_final: 0.6947 (mt) REVERT: C 79 ASN cc_start: 0.7858 (t0) cc_final: 0.7499 (t0) REVERT: C 90 THR cc_start: 0.8627 (p) cc_final: 0.8351 (t) REVERT: C 109 ARG cc_start: 0.8967 (mmt180) cc_final: 0.8409 (tpp-160) REVERT: C 135 HIS cc_start: 0.7391 (p90) cc_final: 0.6966 (p90) REVERT: C 149 PRO cc_start: 0.8671 (Cg_exo) cc_final: 0.8292 (Cg_endo) REVERT: C 179 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7391 (mt-10) REVERT: C 182 HIS cc_start: 0.8156 (m-70) cc_final: 0.7380 (m170) REVERT: C 203 GLN cc_start: 0.9031 (tp40) cc_final: 0.8096 (tp40) REVERT: C 204 ASP cc_start: 0.8678 (m-30) cc_final: 0.8311 (m-30) REVERT: C 227 ARG cc_start: 0.8735 (mtt180) cc_final: 0.7901 (mtt180) REVERT: C 228 GLN cc_start: 0.8516 (tt0) cc_final: 0.8109 (tm-30) REVERT: C 230 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7593 (mt-10) REVERT: C 243 LYS cc_start: 0.8743 (tmtt) cc_final: 0.8386 (tptp) REVERT: C 263 TRP cc_start: 0.8306 (m100) cc_final: 0.7751 (m100) REVERT: C 269 ASN cc_start: 0.7539 (m-40) cc_final: 0.6982 (m-40) REVERT: C 279 TRP cc_start: 0.7592 (t-100) cc_final: 0.7349 (t-100) REVERT: D 51 LEU cc_start: 0.7454 (mt) cc_final: 0.7232 (mt) REVERT: D 79 ASN cc_start: 0.7881 (t0) cc_final: 0.7527 (t0) REVERT: D 108 PHE cc_start: 0.8824 (p90) cc_final: 0.8037 (p90) REVERT: D 109 ARG cc_start: 0.9127 (mmt180) cc_final: 0.8735 (mmt180) REVERT: D 129 LYS cc_start: 0.9228 (mttp) cc_final: 0.8960 (mmtm) REVERT: D 135 HIS cc_start: 0.7226 (p-80) cc_final: 0.6787 (p-80) REVERT: D 179 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7312 (mt-10) REVERT: D 203 GLN cc_start: 0.9059 (tp40) cc_final: 0.8403 (tp40) REVERT: D 204 ASP cc_start: 0.8802 (m-30) cc_final: 0.8395 (m-30) REVERT: D 226 ILE cc_start: 0.9024 (tp) cc_final: 0.8810 (tp) REVERT: D 230 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7547 (mt-10) REVERT: D 238 LEU cc_start: 0.9022 (mt) cc_final: 0.8816 (mt) REVERT: D 242 GLN cc_start: 0.8180 (tp40) cc_final: 0.7879 (tp-100) REVERT: D 269 ASN cc_start: 0.7636 (m-40) cc_final: 0.7121 (m-40) REVERT: D 279 TRP cc_start: 0.7843 (t60) cc_final: 0.7605 (t-100) REVERT: A 37 ILE cc_start: 0.8409 (pt) cc_final: 0.8165 (pt) REVERT: A 108 PHE cc_start: 0.8753 (p90) cc_final: 0.7923 (p90) REVERT: A 133 TYR cc_start: 0.8574 (t80) cc_final: 0.8284 (t80) REVERT: A 135 HIS cc_start: 0.7667 (p-80) cc_final: 0.7270 (p90) REVERT: A 140 ASP cc_start: 0.7982 (t0) cc_final: 0.7686 (t0) REVERT: A 176 GLN cc_start: 0.7612 (tm-30) cc_final: 0.7243 (tm-30) REVERT: A 203 GLN cc_start: 0.9011 (tp40) cc_final: 0.8613 (tp40) REVERT: A 204 ASP cc_start: 0.8840 (m-30) cc_final: 0.8543 (m-30) REVERT: A 226 ILE cc_start: 0.9060 (tp) cc_final: 0.8625 (tp) REVERT: A 227 ARG cc_start: 0.8644 (mtt180) cc_final: 0.8249 (mtt180) REVERT: A 228 GLN cc_start: 0.8409 (tt0) cc_final: 0.8139 (tm-30) REVERT: A 230 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7252 (mt-10) REVERT: A 255 LYS cc_start: 0.8782 (pttm) cc_final: 0.8555 (ptpp) REVERT: A 260 ASP cc_start: 0.7940 (t0) cc_final: 0.7580 (t0) REVERT: A 261 LEU cc_start: 0.8226 (pt) cc_final: 0.7870 (pt) REVERT: A 269 ASN cc_start: 0.7597 (m-40) cc_final: 0.6977 (m-40) REVERT: E 51 LEU cc_start: 0.7602 (mt) cc_final: 0.7362 (mt) REVERT: E 63 GLN cc_start: 0.8785 (mt0) cc_final: 0.8404 (mt0) REVERT: E 79 ASN cc_start: 0.8013 (t0) cc_final: 0.7510 (t0) REVERT: E 133 TYR cc_start: 0.8652 (t80) cc_final: 0.8370 (t80) REVERT: E 176 GLN cc_start: 0.7697 (tm-30) cc_final: 0.7440 (tm-30) REVERT: E 203 GLN cc_start: 0.9026 (tp40) cc_final: 0.8413 (tp40) REVERT: E 204 ASP cc_start: 0.8668 (m-30) cc_final: 0.8342 (m-30) REVERT: E 230 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7358 (tm-30) REVERT: E 269 ASN cc_start: 0.7692 (m-40) cc_final: 0.7058 (m-40) REVERT: F 51 LEU cc_start: 0.7524 (mt) cc_final: 0.7301 (mt) REVERT: F 79 ASN cc_start: 0.7846 (t0) cc_final: 0.7442 (t0) REVERT: F 108 PHE cc_start: 0.8903 (p90) cc_final: 0.8689 (p90) REVERT: F 129 LYS cc_start: 0.9216 (mttp) cc_final: 0.8940 (tppt) REVERT: F 203 GLN cc_start: 0.8976 (tp40) cc_final: 0.8148 (tp40) REVERT: F 204 ASP cc_start: 0.8845 (m-30) cc_final: 0.8361 (m-30) REVERT: F 226 ILE cc_start: 0.9005 (tp) cc_final: 0.8755 (tp) REVERT: F 228 GLN cc_start: 0.8482 (tt0) cc_final: 0.8046 (tm-30) REVERT: F 230 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7504 (mt-10) REVERT: F 238 LEU cc_start: 0.8988 (mt) cc_final: 0.8768 (mt) REVERT: F 269 ASN cc_start: 0.8238 (m-40) cc_final: 0.7392 (m-40) REVERT: G 46 THR cc_start: 0.8235 (t) cc_final: 0.7737 (p) REVERT: G 54 HIS cc_start: 0.7360 (m-70) cc_final: 0.7153 (m-70) REVERT: G 60 LEU cc_start: 0.8968 (mm) cc_final: 0.8763 (mt) REVERT: G 79 ASN cc_start: 0.8173 (t0) cc_final: 0.7811 (t0) REVERT: G 116 THR cc_start: 0.8696 (t) cc_final: 0.8189 (t) REVERT: G 117 GLN cc_start: 0.8272 (mm110) cc_final: 0.8007 (mm110) REVERT: G 129 LYS cc_start: 0.9298 (ptpp) cc_final: 0.8976 (mttp) REVERT: G 135 HIS cc_start: 0.7652 (p-80) cc_final: 0.7203 (p90) REVERT: G 141 ASN cc_start: 0.8862 (t0) cc_final: 0.8530 (t0) REVERT: G 149 PRO cc_start: 0.9009 (Cg_exo) cc_final: 0.8653 (Cg_endo) REVERT: G 179 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7093 (mt-10) REVERT: G 182 HIS cc_start: 0.8153 (m-70) cc_final: 0.7471 (m170) REVERT: G 183 GLN cc_start: 0.5078 (pm20) cc_final: 0.4821 (pm20) REVERT: G 203 GLN cc_start: 0.9147 (tp40) cc_final: 0.7966 (tp40) REVERT: G 204 ASP cc_start: 0.8820 (m-30) cc_final: 0.8576 (m-30) REVERT: G 226 ILE cc_start: 0.8940 (tp) cc_final: 0.8680 (tp) REVERT: G 227 ARG cc_start: 0.8851 (mtt180) cc_final: 0.8039 (mtt180) REVERT: G 228 GLN cc_start: 0.8431 (tt0) cc_final: 0.7956 (tm-30) REVERT: G 230 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7575 (mt-10) REVERT: G 238 LEU cc_start: 0.8774 (mt) cc_final: 0.8471 (mp) REVERT: G 263 TRP cc_start: 0.8257 (m100) cc_final: 0.7734 (m100) REVERT: G 269 ASN cc_start: 0.7501 (m-40) cc_final: 0.6926 (m-40) outliers start: 0 outliers final: 0 residues processed: 433 average time/residue: 0.3051 time to fit residues: 190.1708 Evaluate side-chains 402 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 123 optimal weight: 0.0670 chunk 95 optimal weight: 0.2980 chunk 142 optimal weight: 0.0870 chunk 94 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 B 273 GLN C 63 GLN C 228 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN D 135 HIS D 146 HIS D 228 GLN D 273 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS A 228 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN E 135 HIS E 146 HIS F 63 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 GLN 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16772 Z= 0.270 Angle : 0.845 10.221 23765 Z= 0.328 Chirality : 0.047 0.135 2128 Planarity : 0.004 0.042 2912 Dihedral : 17.938 89.448 2303 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % 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 : 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: -2.16 (0.20), residues: 1792 helix: -1.86 (0.25), residues: 301 sheet: -1.78 (0.58), residues: 70 loop : -1.42 (0.18), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 279 HIS 0.008 0.001 HIS A 64 PHE 0.013 0.001 PHE D 103 TYR 0.017 0.002 TYR B 133 ARG 0.003 0.000 ARG E 197 *********************** 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 439 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 1.603 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 51 LEU cc_start: 0.7377 (mt) cc_final: 0.7164 (mt) REVERT: B 63 GLN cc_start: 0.8727 (mt0) cc_final: 0.8321 (mp10) REVERT: B 79 ASN cc_start: 0.7958 (t0) cc_final: 0.7576 (t0) REVERT: B 95 MET cc_start: 0.8707 (mmm) cc_final: 0.8441 (mmp) REVERT: B 135 HIS cc_start: 0.7428 (p90) cc_final: 0.7112 (p90) REVERT: B 176 GLN cc_start: 0.7166 (tm-30) cc_final: 0.6889 (tm-30) REVERT: B 203 GLN cc_start: 0.9066 (tp40) cc_final: 0.8684 (tp40) REVERT: B 204 ASP cc_start: 0.8748 (m-30) cc_final: 0.7958 (t0) REVERT: B 255 LYS cc_start: 0.8853 (pttm) cc_final: 0.8614 (ptpp) REVERT: C 51 LEU cc_start: 0.7217 (mt) cc_final: 0.7007 (mt) REVERT: C 79 ASN cc_start: 0.7835 (t0) cc_final: 0.7477 (t0) REVERT: C 90 THR cc_start: 0.8623 (p) cc_final: 0.8343 (t) REVERT: C 109 ARG cc_start: 0.8881 (mmt180) cc_final: 0.8360 (mmp80) REVERT: C 149 PRO cc_start: 0.8672 (Cg_exo) cc_final: 0.8185 (Cg_endo) REVERT: C 179 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7030 (mt-10) REVERT: C 182 HIS cc_start: 0.8133 (m-70) cc_final: 0.7248 (m170) REVERT: C 183 GLN cc_start: 0.6009 (pm20) cc_final: 0.5242 (pm20) REVERT: C 203 GLN cc_start: 0.9028 (tp40) cc_final: 0.8105 (tp40) REVERT: C 204 ASP cc_start: 0.8657 (m-30) cc_final: 0.8283 (m-30) REVERT: C 230 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7640 (mt-10) REVERT: C 243 LYS cc_start: 0.8726 (tmtt) cc_final: 0.8382 (tptp) REVERT: C 263 TRP cc_start: 0.8289 (m100) cc_final: 0.7750 (m100) REVERT: C 269 ASN cc_start: 0.7551 (m-40) cc_final: 0.6957 (m-40) REVERT: C 279 TRP cc_start: 0.7587 (t-100) cc_final: 0.7344 (t-100) REVERT: D 46 THR cc_start: 0.8076 (t) cc_final: 0.7741 (t) REVERT: D 51 LEU cc_start: 0.7457 (mt) cc_final: 0.7233 (mt) REVERT: D 60 LEU cc_start: 0.9095 (mm) cc_final: 0.8793 (mt) REVERT: D 79 ASN cc_start: 0.7875 (t0) cc_final: 0.7509 (t0) REVERT: D 108 PHE cc_start: 0.8827 (p90) cc_final: 0.8284 (p90) REVERT: D 129 LYS cc_start: 0.9215 (mttp) cc_final: 0.8947 (mmtm) REVERT: D 135 HIS cc_start: 0.7388 (p90) cc_final: 0.6943 (p-80) REVERT: D 179 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7295 (mt-10) REVERT: D 203 GLN cc_start: 0.8865 (tp40) cc_final: 0.8171 (tp40) REVERT: D 204 ASP cc_start: 0.8763 (m-30) cc_final: 0.8385 (m-30) REVERT: D 226 ILE cc_start: 0.9023 (tp) cc_final: 0.8794 (tp) REVERT: D 227 ARG cc_start: 0.8724 (mtt180) cc_final: 0.8273 (mtt180) REVERT: D 228 GLN cc_start: 0.8319 (tt0) cc_final: 0.7762 (tm-30) REVERT: D 230 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7468 (mt-10) REVERT: D 238 LEU cc_start: 0.9008 (mt) cc_final: 0.8791 (mt) REVERT: D 242 GLN cc_start: 0.8206 (tp40) cc_final: 0.7947 (tp-100) REVERT: D 269 ASN cc_start: 0.7631 (m-40) cc_final: 0.7038 (m-40) REVERT: D 279 TRP cc_start: 0.7849 (t60) cc_final: 0.7614 (t-100) REVERT: A 37 ILE cc_start: 0.8371 (pt) cc_final: 0.8135 (pt) REVERT: A 133 TYR cc_start: 0.8567 (t80) cc_final: 0.8265 (t80) REVERT: A 135 HIS cc_start: 0.7649 (p-80) cc_final: 0.7222 (p90) REVERT: A 140 ASP cc_start: 0.8037 (t0) cc_final: 0.7682 (t0) REVERT: A 176 GLN cc_start: 0.7542 (tm-30) cc_final: 0.7259 (tm-30) REVERT: A 203 GLN cc_start: 0.8803 (tp40) cc_final: 0.8335 (tp40) REVERT: A 204 ASP cc_start: 0.8791 (m-30) cc_final: 0.8488 (m-30) REVERT: A 255 LYS cc_start: 0.8808 (pttm) cc_final: 0.8575 (ptpp) REVERT: A 260 ASP cc_start: 0.7932 (t0) cc_final: 0.7579 (t0) REVERT: A 261 LEU cc_start: 0.8203 (pt) cc_final: 0.7834 (pt) REVERT: A 269 ASN cc_start: 0.7466 (m-40) cc_final: 0.7103 (m-40) REVERT: E 51 LEU cc_start: 0.7652 (mt) cc_final: 0.7425 (mt) REVERT: E 63 GLN cc_start: 0.8731 (mt0) cc_final: 0.8374 (mt0) REVERT: E 79 ASN cc_start: 0.7987 (t0) cc_final: 0.7481 (t0) REVERT: E 108 PHE cc_start: 0.8941 (p90) cc_final: 0.8476 (p90) REVERT: E 129 LYS cc_start: 0.9156 (mttp) cc_final: 0.8896 (mmtp) REVERT: E 133 TYR cc_start: 0.8640 (t80) cc_final: 0.8342 (t80) REVERT: E 135 HIS cc_start: 0.7435 (p90) cc_final: 0.7029 (p-80) REVERT: E 139 ILE cc_start: 0.9073 (tp) cc_final: 0.8873 (tp) REVERT: E 203 GLN cc_start: 0.9045 (tp40) cc_final: 0.8433 (tp40) REVERT: E 204 ASP cc_start: 0.8686 (m-30) cc_final: 0.8343 (m-30) REVERT: E 230 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7272 (tm-30) REVERT: E 269 ASN cc_start: 0.7652 (m-40) cc_final: 0.7094 (m-40) REVERT: F 51 LEU cc_start: 0.7594 (mt) cc_final: 0.7371 (mt) REVERT: F 79 ASN cc_start: 0.7825 (t0) cc_final: 0.7403 (t0) REVERT: F 108 PHE cc_start: 0.8917 (p90) cc_final: 0.8677 (p90) REVERT: F 129 LYS cc_start: 0.9228 (mttp) cc_final: 0.8942 (tppt) REVERT: F 203 GLN cc_start: 0.9028 (tp40) cc_final: 0.8222 (tp40) REVERT: F 204 ASP cc_start: 0.8834 (m-30) cc_final: 0.8359 (m-30) REVERT: F 238 LEU cc_start: 0.8999 (mt) cc_final: 0.8781 (mt) REVERT: F 269 ASN cc_start: 0.7776 (m-40) cc_final: 0.7155 (m-40) REVERT: G 46 THR cc_start: 0.8176 (t) cc_final: 0.7704 (p) REVERT: G 54 HIS cc_start: 0.7395 (m-70) cc_final: 0.7158 (m-70) REVERT: G 79 ASN cc_start: 0.8124 (t0) cc_final: 0.7743 (t0) REVERT: G 107 ASP cc_start: 0.8256 (t70) cc_final: 0.7717 (t0) REVERT: G 116 THR cc_start: 0.8698 (t) cc_final: 0.8210 (t) REVERT: G 117 GLN cc_start: 0.8290 (mm110) cc_final: 0.8057 (mm110) REVERT: G 135 HIS cc_start: 0.7556 (p-80) cc_final: 0.7139 (p90) REVERT: G 141 ASN cc_start: 0.8843 (t0) cc_final: 0.8572 (t0) REVERT: G 149 PRO cc_start: 0.8973 (Cg_exo) cc_final: 0.8622 (Cg_endo) REVERT: G 179 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7060 (mt-10) REVERT: G 183 GLN cc_start: 0.5021 (pm20) cc_final: 0.4812 (pm20) REVERT: G 203 GLN cc_start: 0.9170 (tp40) cc_final: 0.7960 (tp40) REVERT: G 204 ASP cc_start: 0.8808 (m-30) cc_final: 0.8443 (m-30) REVERT: G 226 ILE cc_start: 0.8871 (tp) cc_final: 0.8664 (tp) REVERT: G 227 ARG cc_start: 0.8781 (mtt180) cc_final: 0.8228 (mtt180) REVERT: G 230 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7532 (mt-10) REVERT: G 238 LEU cc_start: 0.8806 (mt) cc_final: 0.8554 (mp) REVERT: G 263 TRP cc_start: 0.8232 (m100) cc_final: 0.7743 (m100) REVERT: G 273 GLN cc_start: 0.8096 (mt0) cc_final: 0.7500 (tm-30) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.3057 time to fit residues: 194.2363 Evaluate side-chains 409 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 107 optimal weight: 0.9990 chunk 114 optimal weight: 0.0980 chunk 83 optimal weight: 0.0870 chunk 15 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN B 228 GLN C 228 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 117 GLN D 228 GLN D 273 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN F 63 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 GLN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 HIS G 228 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16772 Z= 0.259 Angle : 0.840 10.476 23765 Z= 0.330 Chirality : 0.047 0.136 2128 Planarity : 0.005 0.042 2912 Dihedral : 17.896 89.941 2303 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.39 % Favored : 87.61 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 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: -2.19 (0.20), residues: 1792 helix: -1.91 (0.25), residues: 301 sheet: -1.85 (0.59), residues: 70 loop : -1.43 (0.18), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 279 HIS 0.010 0.001 HIS A 64 PHE 0.017 0.001 PHE C 108 TYR 0.009 0.001 TYR B 151 ARG 0.005 0.000 ARG A 227 *********************** 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 442 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLN cc_start: 0.8730 (mt0) cc_final: 0.8338 (mp10) REVERT: B 79 ASN cc_start: 0.7962 (t0) cc_final: 0.7529 (t0) REVERT: B 95 MET cc_start: 0.8671 (mmm) cc_final: 0.8455 (mmp) REVERT: B 103 PHE cc_start: 0.8775 (m-80) cc_final: 0.8529 (m-10) REVERT: B 108 PHE cc_start: 0.8903 (p90) cc_final: 0.8627 (p90) REVERT: B 135 HIS cc_start: 0.7328 (p90) cc_final: 0.7078 (p90) REVERT: B 146 HIS cc_start: 0.8186 (p-80) cc_final: 0.7862 (p90) REVERT: B 183 GLN cc_start: 0.7309 (pm20) cc_final: 0.7090 (pm20) REVERT: B 203 GLN cc_start: 0.9083 (tp40) cc_final: 0.8177 (tp40) REVERT: B 204 ASP cc_start: 0.8745 (m-30) cc_final: 0.7831 (t0) REVERT: B 228 GLN cc_start: 0.8347 (tt0) cc_final: 0.8087 (tm-30) REVERT: C 46 THR cc_start: 0.8055 (t) cc_final: 0.7542 (p) REVERT: C 79 ASN cc_start: 0.7804 (t0) cc_final: 0.7440 (t0) REVERT: C 90 THR cc_start: 0.8654 (p) cc_final: 0.8380 (t) REVERT: C 109 ARG cc_start: 0.8875 (mmt180) cc_final: 0.8376 (mmp80) REVERT: C 135 HIS cc_start: 0.7470 (p90) cc_final: 0.7133 (p90) REVERT: C 149 PRO cc_start: 0.8642 (Cg_exo) cc_final: 0.8226 (Cg_endo) REVERT: C 179 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7062 (mt-10) REVERT: C 182 HIS cc_start: 0.8006 (m-70) cc_final: 0.7137 (m170) REVERT: C 183 GLN cc_start: 0.5810 (pm20) cc_final: 0.5211 (pm20) REVERT: C 203 GLN cc_start: 0.9028 (tp40) cc_final: 0.8095 (tp40) REVERT: C 204 ASP cc_start: 0.8669 (m-30) cc_final: 0.8272 (m-30) REVERT: C 227 ARG cc_start: 0.8605 (mtt180) cc_final: 0.8124 (mtt180) REVERT: C 228 GLN cc_start: 0.8415 (tt0) cc_final: 0.8005 (tm-30) REVERT: C 230 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7550 (mt-10) REVERT: C 243 LYS cc_start: 0.8716 (tmtt) cc_final: 0.8361 (tptp) REVERT: C 263 TRP cc_start: 0.8258 (m100) cc_final: 0.7766 (m100) REVERT: C 269 ASN cc_start: 0.7568 (m-40) cc_final: 0.6937 (m-40) REVERT: C 279 TRP cc_start: 0.7573 (t-100) cc_final: 0.7342 (t-100) REVERT: D 54 HIS cc_start: 0.7329 (m-70) cc_final: 0.7057 (m-70) REVERT: D 60 LEU cc_start: 0.9084 (mm) cc_final: 0.8789 (mt) REVERT: D 79 ASN cc_start: 0.7884 (t0) cc_final: 0.7481 (t0) REVERT: D 108 PHE cc_start: 0.8829 (p90) cc_final: 0.7977 (p90) REVERT: D 109 ARG cc_start: 0.9127 (mmt180) cc_final: 0.8740 (mmt180) REVERT: D 129 LYS cc_start: 0.9222 (mttp) cc_final: 0.8958 (mmtm) REVERT: D 179 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7264 (mt-10) REVERT: D 203 GLN cc_start: 0.8853 (tp40) cc_final: 0.8158 (tp40) REVERT: D 204 ASP cc_start: 0.8736 (m-30) cc_final: 0.8345 (m-30) REVERT: D 226 ILE cc_start: 0.9026 (tp) cc_final: 0.8817 (tp) REVERT: D 227 ARG cc_start: 0.8619 (mtt180) cc_final: 0.8414 (mtt180) REVERT: D 230 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7447 (mt-10) REVERT: D 238 LEU cc_start: 0.8988 (mt) cc_final: 0.8761 (mt) REVERT: D 242 GLN cc_start: 0.8181 (tp40) cc_final: 0.7929 (tp-100) REVERT: D 279 TRP cc_start: 0.7796 (t60) cc_final: 0.7568 (t-100) REVERT: A 46 THR cc_start: 0.8092 (t) cc_final: 0.7517 (p) REVERT: A 79 ASN cc_start: 0.7584 (t0) cc_final: 0.7249 (t0) REVERT: A 95 MET cc_start: 0.9016 (mmp) cc_final: 0.8694 (mmm) REVERT: A 133 TYR cc_start: 0.8533 (t80) cc_final: 0.8244 (t80) REVERT: A 135 HIS cc_start: 0.7525 (p-80) cc_final: 0.7163 (p90) REVERT: A 140 ASP cc_start: 0.8092 (t0) cc_final: 0.7739 (t0) REVERT: A 176 GLN cc_start: 0.7653 (tm-30) cc_final: 0.7373 (tm-30) REVERT: A 203 GLN cc_start: 0.8778 (tp40) cc_final: 0.8292 (tp40) REVERT: A 204 ASP cc_start: 0.8781 (m-30) cc_final: 0.8460 (m-30) REVERT: A 230 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7225 (tm-30) REVERT: A 255 LYS cc_start: 0.8821 (pttm) cc_final: 0.8582 (ptpp) REVERT: A 261 LEU cc_start: 0.8136 (pt) cc_final: 0.7870 (pt) REVERT: A 269 ASN cc_start: 0.7594 (m-40) cc_final: 0.6987 (m-40) REVERT: E 46 THR cc_start: 0.8065 (t) cc_final: 0.7556 (p) REVERT: E 51 LEU cc_start: 0.7655 (mt) cc_final: 0.7439 (mt) REVERT: E 60 LEU cc_start: 0.8811 (pp) cc_final: 0.8598 (pp) REVERT: E 62 GLN cc_start: 0.8645 (mm110) cc_final: 0.8227 (mm110) REVERT: E 63 GLN cc_start: 0.8731 (mt0) cc_final: 0.8338 (mt0) REVERT: E 79 ASN cc_start: 0.7967 (t0) cc_final: 0.7407 (t0) REVERT: E 108 PHE cc_start: 0.8867 (p90) cc_final: 0.8554 (p90) REVERT: E 129 LYS cc_start: 0.9130 (mttp) cc_final: 0.8851 (mmtp) REVERT: E 133 TYR cc_start: 0.8625 (t80) cc_final: 0.8314 (t80) REVERT: E 149 PRO cc_start: 0.8798 (Cg_exo) cc_final: 0.8033 (Cg_endo) REVERT: E 203 GLN cc_start: 0.9059 (tp40) cc_final: 0.8431 (tp40) REVERT: E 204 ASP cc_start: 0.8682 (m-30) cc_final: 0.8329 (m-30) REVERT: E 230 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7194 (tm-30) REVERT: E 269 ASN cc_start: 0.7629 (m-40) cc_final: 0.7086 (m-40) REVERT: F 79 ASN cc_start: 0.7811 (t0) cc_final: 0.7381 (t0) REVERT: F 108 PHE cc_start: 0.8914 (p90) cc_final: 0.8657 (p90) REVERT: F 129 LYS cc_start: 0.9231 (mttp) cc_final: 0.8951 (tppt) REVERT: F 183 GLN cc_start: 0.7205 (pm20) cc_final: 0.6747 (pm20) REVERT: F 203 GLN cc_start: 0.9041 (tp40) cc_final: 0.8288 (tp40) REVERT: F 228 GLN cc_start: 0.8361 (tt0) cc_final: 0.7966 (tm-30) REVERT: F 230 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7721 (mt-10) REVERT: F 261 LEU cc_start: 0.7969 (pt) cc_final: 0.7695 (pt) REVERT: F 269 ASN cc_start: 0.8194 (m-40) cc_final: 0.7347 (m-40) REVERT: G 46 THR cc_start: 0.8175 (t) cc_final: 0.7678 (p) REVERT: G 62 GLN cc_start: 0.8711 (mm110) cc_final: 0.8277 (mm110) REVERT: G 79 ASN cc_start: 0.8173 (t0) cc_final: 0.7746 (t0) REVERT: G 107 ASP cc_start: 0.8180 (t70) cc_final: 0.7659 (t0) REVERT: G 116 THR cc_start: 0.8709 (t) cc_final: 0.8218 (t) REVERT: G 117 GLN cc_start: 0.8291 (mm110) cc_final: 0.8051 (mm110) REVERT: G 135 HIS cc_start: 0.7502 (p-80) cc_final: 0.7121 (p90) REVERT: G 141 ASN cc_start: 0.8830 (t0) cc_final: 0.8518 (t0) REVERT: G 149 PRO cc_start: 0.8946 (Cg_exo) cc_final: 0.8551 (Cg_endo) REVERT: G 179 GLU cc_start: 0.7685 (mt-10) cc_final: 0.6992 (mt-10) REVERT: G 203 GLN cc_start: 0.9187 (tp40) cc_final: 0.7910 (tp40) REVERT: G 204 ASP cc_start: 0.8794 (m-30) cc_final: 0.8539 (m-30) REVERT: G 226 ILE cc_start: 0.8869 (tp) cc_final: 0.8630 (tp) REVERT: G 227 ARG cc_start: 0.8606 (mtt180) cc_final: 0.7885 (mtt180) REVERT: G 228 GLN cc_start: 0.8472 (tt0) cc_final: 0.8006 (tm-30) REVERT: G 230 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7449 (mt-10) REVERT: G 263 TRP cc_start: 0.8185 (m100) cc_final: 0.7752 (m100) REVERT: G 273 GLN cc_start: 0.8086 (mt0) cc_final: 0.7502 (tm-30) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.3042 time to fit residues: 194.1891 Evaluate side-chains 407 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 0.6980 chunk 147 optimal weight: 0.6980 chunk 157 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 142 optimal weight: 0.0470 chunk 148 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN B 228 GLN C 63 GLN C 228 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 117 GLN D 135 HIS D 146 HIS ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 GLN E 135 HIS F 54 HIS ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 GLN F 273 GLN ** G 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 HIS G 228 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 16772 Z= 0.293 Angle : 0.861 9.954 23765 Z= 0.337 Chirality : 0.047 0.146 2128 Planarity : 0.005 0.042 2912 Dihedral : 17.833 89.940 2303 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % 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: -2.22 (0.20), residues: 1792 helix: -1.91 (0.26), residues: 301 sheet: -1.97 (0.58), residues: 70 loop : -1.45 (0.18), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 279 HIS 0.010 0.001 HIS A 64 PHE 0.012 0.001 PHE B 200 TYR 0.018 0.002 TYR B 133 ARG 0.005 0.001 ARG B 197 *********************** 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 449 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 1.603 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: 0.8075 (t) cc_final: 0.7649 (p) REVERT: B 51 LEU cc_start: 0.7415 (mt) cc_final: 0.7188 (mt) REVERT: B 63 GLN cc_start: 0.8812 (mt0) cc_final: 0.8390 (mt0) REVERT: B 79 ASN cc_start: 0.7987 (t0) cc_final: 0.7584 (t0) REVERT: B 95 MET cc_start: 0.8668 (mmm) cc_final: 0.8416 (mmp) REVERT: B 108 PHE cc_start: 0.8947 (p90) cc_final: 0.8730 (p90) REVERT: B 135 HIS cc_start: 0.7312 (p90) cc_final: 0.7099 (p90) REVERT: B 146 HIS cc_start: 0.8194 (p-80) cc_final: 0.7912 (p90) REVERT: B 176 GLN cc_start: 0.7157 (tm-30) cc_final: 0.6702 (tm-30) REVERT: B 197 ARG cc_start: 0.7014 (ttt180) cc_final: 0.6782 (ttt180) REVERT: B 200 PHE cc_start: 0.7658 (m-10) cc_final: 0.7134 (m-10) REVERT: B 203 GLN cc_start: 0.9080 (tp40) cc_final: 0.8343 (tp40) REVERT: B 204 ASP cc_start: 0.8744 (m-30) cc_final: 0.7729 (t0) REVERT: B 255 LYS cc_start: 0.8884 (pttm) cc_final: 0.8656 (ptpp) REVERT: C 54 HIS cc_start: 0.7380 (m-70) cc_final: 0.7090 (m-70) REVERT: C 90 THR cc_start: 0.8675 (p) cc_final: 0.8410 (t) REVERT: C 109 ARG cc_start: 0.8864 (mmt180) cc_final: 0.8177 (mmp80) REVERT: C 149 PRO cc_start: 0.8760 (Cg_exo) cc_final: 0.8414 (Cg_endo) REVERT: C 179 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7327 (mt-10) REVERT: C 182 HIS cc_start: 0.8059 (m-70) cc_final: 0.7158 (m170) REVERT: C 183 GLN cc_start: 0.5805 (pm20) cc_final: 0.5301 (pm20) REVERT: C 203 GLN cc_start: 0.8883 (tp40) cc_final: 0.7837 (tp40) REVERT: C 204 ASP cc_start: 0.8643 (m-30) cc_final: 0.8268 (m-30) REVERT: C 226 ILE cc_start: 0.9040 (tp) cc_final: 0.8677 (tp) REVERT: C 227 ARG cc_start: 0.8661 (mtt180) cc_final: 0.8302 (mtt180) REVERT: C 230 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7435 (mt-10) REVERT: C 236 ASN cc_start: 0.8635 (p0) cc_final: 0.8316 (t0) REVERT: C 243 LYS cc_start: 0.8737 (tmtt) cc_final: 0.8358 (tptp) REVERT: C 255 LYS cc_start: 0.8749 (ptpp) cc_final: 0.8507 (ptpp) REVERT: C 263 TRP cc_start: 0.8304 (m100) cc_final: 0.7766 (m100) REVERT: C 269 ASN cc_start: 0.7593 (m-40) cc_final: 0.7056 (m-40) REVERT: D 54 HIS cc_start: 0.7371 (m-70) cc_final: 0.7078 (m-70) REVERT: D 60 LEU cc_start: 0.9103 (mm) cc_final: 0.8831 (mt) REVERT: D 79 ASN cc_start: 0.7913 (t0) cc_final: 0.7541 (t0) REVERT: D 107 ASP cc_start: 0.8260 (t70) cc_final: 0.8053 (t0) REVERT: D 108 PHE cc_start: 0.8846 (p90) cc_final: 0.8629 (p90) REVERT: D 109 ARG cc_start: 0.9152 (mmt180) cc_final: 0.8898 (mmt180) REVERT: D 129 LYS cc_start: 0.9214 (mttp) cc_final: 0.8871 (mmtm) REVERT: D 135 HIS cc_start: 0.7415 (p90) cc_final: 0.7104 (p-80) REVERT: D 149 PRO cc_start: 0.8980 (Cg_exo) cc_final: 0.8713 (Cg_endo) REVERT: D 179 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7282 (mt-10) REVERT: D 183 GLN cc_start: 0.7050 (pm20) cc_final: 0.6454 (pm20) REVERT: D 203 GLN cc_start: 0.8838 (tp40) cc_final: 0.8181 (tp40) REVERT: D 204 ASP cc_start: 0.8784 (m-30) cc_final: 0.8553 (m-30) REVERT: D 213 ASP cc_start: 0.8687 (t0) cc_final: 0.8295 (t0) REVERT: D 227 ARG cc_start: 0.8638 (mtt180) cc_final: 0.8219 (mtt180) REVERT: D 230 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7336 (mt-10) REVERT: D 238 LEU cc_start: 0.8983 (mt) cc_final: 0.8754 (mt) REVERT: D 242 GLN cc_start: 0.8233 (tp40) cc_final: 0.7924 (tp-100) REVERT: D 244 ASP cc_start: 0.8301 (t0) cc_final: 0.8023 (t0) REVERT: D 260 ASP cc_start: 0.8026 (t0) cc_final: 0.7753 (t0) REVERT: D 261 LEU cc_start: 0.8304 (pt) cc_final: 0.7927 (pt) REVERT: D 279 TRP cc_start: 0.7827 (t60) cc_final: 0.7568 (t-100) REVERT: A 54 HIS cc_start: 0.7544 (m-70) cc_final: 0.7137 (m-70) REVERT: A 79 ASN cc_start: 0.7669 (t0) cc_final: 0.7302 (t0) REVERT: A 95 MET cc_start: 0.9024 (mmp) cc_final: 0.8708 (mmm) REVERT: A 133 TYR cc_start: 0.8576 (t80) cc_final: 0.8293 (t80) REVERT: A 135 HIS cc_start: 0.7531 (p-80) cc_final: 0.7247 (p90) REVERT: A 146 HIS cc_start: 0.8033 (p90) cc_final: 0.7751 (p90) REVERT: A 176 GLN cc_start: 0.7372 (tm-30) cc_final: 0.7080 (tm-30) REVERT: A 203 GLN cc_start: 0.8861 (tp40) cc_final: 0.8344 (tp40) REVERT: A 204 ASP cc_start: 0.8809 (m-30) cc_final: 0.8489 (m-30) REVERT: A 230 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7201 (tm-30) REVERT: A 255 LYS cc_start: 0.8789 (pttm) cc_final: 0.8581 (ptpp) REVERT: A 269 ASN cc_start: 0.8050 (m-40) cc_final: 0.7273 (m-40) REVERT: A 279 TRP cc_start: 0.7571 (t-100) cc_final: 0.7278 (t-100) REVERT: E 46 THR cc_start: 0.8137 (t) cc_final: 0.7590 (p) REVERT: E 51 LEU cc_start: 0.7668 (mt) cc_final: 0.7447 (mt) REVERT: E 60 LEU cc_start: 0.8783 (pp) cc_final: 0.8493 (pp) REVERT: E 62 GLN cc_start: 0.8630 (mm110) cc_final: 0.8225 (mm110) REVERT: E 63 GLN cc_start: 0.8762 (mt0) cc_final: 0.8343 (mt0) REVERT: E 108 PHE cc_start: 0.8814 (p90) cc_final: 0.8560 (p90) REVERT: E 109 ARG cc_start: 0.8633 (mmm-85) cc_final: 0.8363 (mmm160) REVERT: E 129 LYS cc_start: 0.9109 (mttp) cc_final: 0.8809 (mmtp) REVERT: E 133 TYR cc_start: 0.8651 (t80) cc_final: 0.8356 (t80) REVERT: E 135 HIS cc_start: 0.7456 (p90) cc_final: 0.7101 (p-80) REVERT: E 149 PRO cc_start: 0.8954 (Cg_exo) cc_final: 0.7905 (Cg_endo) REVERT: E 182 HIS cc_start: 0.7645 (m170) cc_final: 0.7335 (m170) REVERT: E 203 GLN cc_start: 0.9028 (tp40) cc_final: 0.8367 (tp40) REVERT: E 204 ASP cc_start: 0.8705 (m-30) cc_final: 0.8342 (m-30) REVERT: E 227 ARG cc_start: 0.9022 (mtt180) cc_final: 0.8776 (mmm160) REVERT: E 263 TRP cc_start: 0.8245 (m100) cc_final: 0.8032 (m100) REVERT: E 269 ASN cc_start: 0.7589 (m-40) cc_final: 0.7189 (m-40) REVERT: F 79 ASN cc_start: 0.7849 (t0) cc_final: 0.7389 (t0) REVERT: F 108 PHE cc_start: 0.8926 (p90) cc_final: 0.8665 (p90) REVERT: F 129 LYS cc_start: 0.9211 (mttp) cc_final: 0.8930 (tppt) REVERT: F 183 GLN cc_start: 0.7123 (pm20) cc_final: 0.6597 (pm20) REVERT: F 203 GLN cc_start: 0.9127 (tp40) cc_final: 0.8346 (tp40) REVERT: F 227 ARG cc_start: 0.8793 (mtt180) cc_final: 0.8284 (mmt90) REVERT: F 228 GLN cc_start: 0.8105 (tt0) cc_final: 0.7828 (tm-30) REVERT: F 230 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7711 (mt-10) REVERT: F 269 ASN cc_start: 0.7692 (m-40) cc_final: 0.7043 (m-40) REVERT: F 277 TRP cc_start: 0.7897 (t-100) cc_final: 0.7369 (t-100) REVERT: G 46 THR cc_start: 0.8311 (t) cc_final: 0.7815 (p) REVERT: G 54 HIS cc_start: 0.7495 (m-70) cc_final: 0.7171 (m-70) REVERT: G 79 ASN cc_start: 0.8265 (t0) cc_final: 0.7921 (t0) REVERT: G 107 ASP cc_start: 0.8240 (t70) cc_final: 0.7746 (t0) REVERT: G 116 THR cc_start: 0.8728 (t) cc_final: 0.8271 (t) REVERT: G 117 GLN cc_start: 0.8307 (mm110) cc_final: 0.8081 (mm110) REVERT: G 135 HIS cc_start: 0.7562 (p-80) cc_final: 0.7267 (p90) REVERT: G 141 ASN cc_start: 0.8822 (t0) cc_final: 0.8540 (t0) REVERT: G 148 ILE cc_start: 0.9104 (mm) cc_final: 0.8896 (mm) REVERT: G 149 PRO cc_start: 0.8941 (Cg_exo) cc_final: 0.8589 (Cg_endo) REVERT: G 179 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7134 (mt-10) REVERT: G 182 HIS cc_start: 0.8339 (m-70) cc_final: 0.7590 (m170) REVERT: G 204 ASP cc_start: 0.8810 (m-30) cc_final: 0.8456 (m-30) REVERT: G 238 LEU cc_start: 0.8746 (mt) cc_final: 0.8501 (mt) REVERT: G 263 TRP cc_start: 0.8237 (m100) cc_final: 0.8006 (m100) REVERT: G 273 GLN cc_start: 0.8114 (mt0) cc_final: 0.7536 (tm-30) outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.2987 time to fit residues: 193.0576 Evaluate side-chains 407 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.2980 chunk 101 optimal weight: 0.0670 chunk 78 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 174 optimal weight: 0.5980 chunk 160 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 14 optimal weight: 0.0050 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.3932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN B 228 GLN C 228 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 117 GLN ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN E 117 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16772 Z= 0.261 Angle : 0.848 10.109 23765 Z= 0.337 Chirality : 0.047 0.133 2128 Planarity : 0.005 0.041 2912 Dihedral : 17.833 89.700 2303 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % 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: -2.29 (0.20), residues: 1792 helix: -2.05 (0.25), residues: 301 sheet: -2.03 (0.57), residues: 70 loop : -1.48 (0.18), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 279 HIS 0.013 0.001 HIS A 64 PHE 0.018 0.001 PHE C 108 TYR 0.011 0.002 TYR B 133 ARG 0.004 0.001 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 THR cc_start: 0.8215 (t) cc_final: 0.7743 (p) REVERT: B 51 LEU cc_start: 0.7345 (mt) cc_final: 0.7123 (mt) REVERT: B 63 GLN cc_start: 0.8781 (mt0) cc_final: 0.8308 (mp10) REVERT: B 79 ASN cc_start: 0.7954 (t0) cc_final: 0.7529 (t0) REVERT: B 95 MET cc_start: 0.8646 (mmm) cc_final: 0.8444 (mmp) REVERT: B 146 HIS cc_start: 0.8210 (p-80) cc_final: 0.7946 (p90) REVERT: B 148 ILE cc_start: 0.9177 (mm) cc_final: 0.8930 (mm) REVERT: B 197 ARG cc_start: 0.7069 (ttt180) cc_final: 0.6848 (ttt180) REVERT: B 200 PHE cc_start: 0.7616 (m-10) cc_final: 0.7089 (m-10) REVERT: B 203 GLN cc_start: 0.9052 (tp40) cc_final: 0.8260 (tp40) REVERT: B 204 ASP cc_start: 0.8688 (m-30) cc_final: 0.7703 (t0) REVERT: B 225 PRO cc_start: 0.8005 (Cg_exo) cc_final: 0.7600 (Cg_endo) REVERT: B 228 GLN cc_start: 0.8307 (tt0) cc_final: 0.7833 (tm-30) REVERT: B 230 GLU cc_start: 0.8272 (tt0) cc_final: 0.7978 (tt0) REVERT: B 255 LYS cc_start: 0.8932 (pttm) cc_final: 0.8693 (ptpp) REVERT: C 46 THR cc_start: 0.8186 (t) cc_final: 0.7898 (t) REVERT: C 90 THR cc_start: 0.8654 (p) cc_final: 0.8407 (t) REVERT: C 149 PRO cc_start: 0.8712 (Cg_exo) cc_final: 0.8356 (Cg_endo) REVERT: C 179 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7085 (mt-10) REVERT: C 182 HIS cc_start: 0.8046 (m-70) cc_final: 0.7163 (m170) REVERT: C 183 GLN cc_start: 0.5731 (pm20) cc_final: 0.5267 (pm20) REVERT: C 203 GLN cc_start: 0.8837 (tp40) cc_final: 0.7815 (tp40) REVERT: C 204 ASP cc_start: 0.8620 (m-30) cc_final: 0.8230 (m-30) REVERT: C 227 ARG cc_start: 0.8627 (mtt180) cc_final: 0.8262 (mtt180) REVERT: C 228 GLN cc_start: 0.8463 (tt0) cc_final: 0.8067 (tm-30) REVERT: C 230 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7693 (mt-10) REVERT: C 236 ASN cc_start: 0.8612 (p0) cc_final: 0.8280 (t0) REVERT: C 243 LYS cc_start: 0.8716 (tmtt) cc_final: 0.8356 (tptp) REVERT: C 255 LYS cc_start: 0.8760 (ptpp) cc_final: 0.8505 (ptpp) REVERT: C 263 TRP cc_start: 0.8251 (m100) cc_final: 0.7743 (m100) REVERT: C 269 ASN cc_start: 0.7573 (m-40) cc_final: 0.7041 (m-40) REVERT: D 46 THR cc_start: 0.7719 (t) cc_final: 0.7465 (t) REVERT: D 54 HIS cc_start: 0.7301 (m-70) cc_final: 0.6959 (m-70) REVERT: D 60 LEU cc_start: 0.9095 (mm) cc_final: 0.8869 (mt) REVERT: D 79 ASN cc_start: 0.7906 (t0) cc_final: 0.7538 (t0) REVERT: D 107 ASP cc_start: 0.8381 (t70) cc_final: 0.7902 (t0) REVERT: D 108 PHE cc_start: 0.8845 (p90) cc_final: 0.8088 (p90) REVERT: D 109 ARG cc_start: 0.9148 (mmt180) cc_final: 0.8815 (mmt180) REVERT: D 117 GLN cc_start: 0.8650 (tp-100) cc_final: 0.8432 (tp-100) REVERT: D 129 LYS cc_start: 0.9201 (mttp) cc_final: 0.8913 (mmtm) REVERT: D 149 PRO cc_start: 0.8949 (Cg_exo) cc_final: 0.8591 (Cg_endo) REVERT: D 179 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7186 (mt-10) REVERT: D 183 GLN cc_start: 0.6972 (pm20) cc_final: 0.6331 (pm20) REVERT: D 203 GLN cc_start: 0.8818 (tp40) cc_final: 0.8170 (tp40) REVERT: D 204 ASP cc_start: 0.8722 (m-30) cc_final: 0.8381 (m-30) REVERT: D 213 ASP cc_start: 0.8639 (t0) cc_final: 0.8246 (t0) REVERT: D 226 ILE cc_start: 0.9104 (tp) cc_final: 0.8893 (tp) REVERT: D 228 GLN cc_start: 0.7475 (tm-30) cc_final: 0.7138 (tm-30) REVERT: D 230 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7367 (mt-10) REVERT: D 242 GLN cc_start: 0.8266 (tp40) cc_final: 0.7923 (tp-100) REVERT: D 244 ASP cc_start: 0.8297 (t0) cc_final: 0.8030 (t0) REVERT: D 260 ASP cc_start: 0.8021 (t0) cc_final: 0.7729 (t0) REVERT: D 261 LEU cc_start: 0.8184 (pt) cc_final: 0.7788 (pt) REVERT: D 269 ASN cc_start: 0.7523 (m-40) cc_final: 0.7231 (m-40) REVERT: D 279 TRP cc_start: 0.7758 (t60) cc_final: 0.7511 (t-100) REVERT: A 54 HIS cc_start: 0.7473 (m-70) cc_final: 0.7008 (m-70) REVERT: A 95 MET cc_start: 0.9022 (mmp) cc_final: 0.8708 (mmm) REVERT: A 108 PHE cc_start: 0.8804 (p90) cc_final: 0.8587 (p90) REVERT: A 133 TYR cc_start: 0.8550 (t80) cc_final: 0.8270 (t80) REVERT: A 135 HIS cc_start: 0.7404 (p-80) cc_final: 0.7156 (p90) REVERT: A 146 HIS cc_start: 0.8071 (p90) cc_final: 0.7707 (p90) REVERT: A 204 ASP cc_start: 0.8779 (m-30) cc_final: 0.8477 (m-30) REVERT: A 230 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7094 (tm-30) REVERT: A 269 ASN cc_start: 0.7465 (m-40) cc_final: 0.6820 (m-40) REVERT: A 279 TRP cc_start: 0.7529 (t-100) cc_final: 0.7280 (t-100) REVERT: E 37 ILE cc_start: 0.7974 (pt) cc_final: 0.7508 (mt) REVERT: E 46 THR cc_start: 0.8110 (t) cc_final: 0.7559 (p) REVERT: E 51 LEU cc_start: 0.7641 (mt) cc_final: 0.7420 (mt) REVERT: E 60 LEU cc_start: 0.8804 (pp) cc_final: 0.8532 (pp) REVERT: E 62 GLN cc_start: 0.8623 (mm110) cc_final: 0.8232 (mm110) REVERT: E 63 GLN cc_start: 0.8759 (mt0) cc_final: 0.8318 (mt0) REVERT: E 79 ASN cc_start: 0.7744 (t0) cc_final: 0.7372 (t0) REVERT: E 108 PHE cc_start: 0.8811 (p90) cc_final: 0.8570 (p90) REVERT: E 109 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8372 (mmm160) REVERT: E 129 LYS cc_start: 0.9110 (mttp) cc_final: 0.8839 (mmtp) REVERT: E 133 TYR cc_start: 0.8597 (t80) cc_final: 0.8300 (t80) REVERT: E 182 HIS cc_start: 0.7646 (m170) cc_final: 0.7354 (m170) REVERT: E 203 GLN cc_start: 0.9015 (tp40) cc_final: 0.8416 (tp40) REVERT: E 227 ARG cc_start: 0.8989 (mtt180) cc_final: 0.8377 (mmt180) REVERT: E 263 TRP cc_start: 0.8246 (m100) cc_final: 0.8015 (m100) REVERT: E 269 ASN cc_start: 0.8097 (m-40) cc_final: 0.7272 (m-40) REVERT: F 54 HIS cc_start: 0.7421 (m-70) cc_final: 0.7122 (m-70) REVERT: F 61 VAL cc_start: 0.8968 (p) cc_final: 0.8766 (m) REVERT: F 79 ASN cc_start: 0.7782 (t0) cc_final: 0.7345 (t0) REVERT: F 108 PHE cc_start: 0.8925 (p90) cc_final: 0.8700 (p90) REVERT: F 129 LYS cc_start: 0.9202 (mttp) cc_final: 0.8928 (tppt) REVERT: F 179 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7181 (mt-10) REVERT: F 183 GLN cc_start: 0.7080 (pm20) cc_final: 0.6780 (pm20) REVERT: F 203 GLN cc_start: 0.9149 (tp40) cc_final: 0.8342 (tp40) REVERT: F 227 ARG cc_start: 0.8759 (mtt180) cc_final: 0.8252 (mmt90) REVERT: F 228 GLN cc_start: 0.8153 (tt0) cc_final: 0.7826 (tm-30) REVERT: F 230 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7634 (mt-10) REVERT: F 269 ASN cc_start: 0.8140 (m-40) cc_final: 0.7251 (m-40) REVERT: F 277 TRP cc_start: 0.7902 (t-100) cc_final: 0.7375 (t-100) REVERT: F 279 TRP cc_start: 0.7695 (t60) cc_final: 0.7354 (t60) REVERT: G 46 THR cc_start: 0.8244 (t) cc_final: 0.7519 (p) REVERT: G 54 HIS cc_start: 0.7402 (m-70) cc_final: 0.7012 (m-70) REVERT: G 79 ASN cc_start: 0.8290 (t0) cc_final: 0.7869 (t0) REVERT: G 116 THR cc_start: 0.8716 (t) cc_final: 0.8249 (t) REVERT: G 117 GLN cc_start: 0.8313 (mm110) cc_final: 0.8097 (mm110) REVERT: G 135 HIS cc_start: 0.7475 (p-80) cc_final: 0.7120 (p-80) REVERT: G 141 ASN cc_start: 0.8790 (t0) cc_final: 0.8580 (t0) REVERT: G 149 PRO cc_start: 0.8918 (Cg_exo) cc_final: 0.8595 (Cg_endo) REVERT: G 179 GLU cc_start: 0.7642 (mt-10) cc_final: 0.6974 (mt-10) REVERT: G 182 HIS cc_start: 0.8229 (m-70) cc_final: 0.7522 (m170) REVERT: G 183 GLN cc_start: 0.7203 (pm20) cc_final: 0.6728 (pm20) REVERT: G 203 GLN cc_start: 0.9199 (tp40) cc_final: 0.7888 (tp40) REVERT: G 204 ASP cc_start: 0.8757 (m-30) cc_final: 0.7912 (t0) REVERT: G 216 LEU cc_start: 0.9036 (tt) cc_final: 0.8494 (mm) REVERT: G 228 GLN cc_start: 0.8462 (tt0) cc_final: 0.7751 (tm-30) REVERT: G 230 GLU cc_start: 0.7502 (tp30) cc_final: 0.7254 (tp30) REVERT: G 238 LEU cc_start: 0.8682 (mt) cc_final: 0.8430 (mt) REVERT: G 269 ASN cc_start: 0.7501 (m-40) cc_final: 0.6851 (m-40) outliers start: 0 outliers final: 0 residues processed: 448 average time/residue: 0.2984 time to fit residues: 192.9336 Evaluate side-chains 412 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 139 optimal weight: 0.0270 chunk 58 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.8642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN B 228 GLN C 228 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 135 HIS D 146 HIS ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 GLN F 273 GLN ** G 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.084131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.069372 restraints weight = 47215.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.072329 restraints weight = 26471.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.074390 restraints weight = 17336.845| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 16772 Z= 0.384 Angle : 0.918 10.164 23765 Z= 0.364 Chirality : 0.049 0.223 2128 Planarity : 0.005 0.041 2912 Dihedral : 18.136 89.961 2303 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.34 % Favored : 86.66 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -2.68 (0.20), residues: 1792 helix: -2.12 (0.26), residues: 301 sheet: -2.28 (0.34), residues: 154 loop : -1.75 (0.18), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 279 HIS 0.010 0.001 HIS A 64 PHE 0.015 0.002 PHE E 34 TYR 0.015 0.002 TYR B 151 ARG 0.009 0.001 ARG G 109 =============================================================================== Job complete usr+sys time: 4040.81 seconds wall clock time: 74 minutes 31.85 seconds (4471.85 seconds total)