Starting phenix.real_space_refine on Sun Apr 27 16:58:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k44_36872/04_2025/8k44_36872.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k44_36872/04_2025/8k44_36872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k44_36872/04_2025/8k44_36872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k44_36872/04_2025/8k44_36872.map" model { file = "/net/cci-nas-00/data/ceres_data/8k44_36872/04_2025/8k44_36872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k44_36872/04_2025/8k44_36872.cif" } resolution = 3.8 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4053 2.51 5 N 1038 2.21 5 O 1236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6360 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2120 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 11, 'TRANS': 268} Chain: "B" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2120 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 11, 'TRANS': 268} Chain: "C" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2120 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 11, 'TRANS': 268} Time building chain proxies: 4.33, per 1000 atoms: 0.68 Number of scatterers: 6360 At special positions: 0 Unit cell: (91.2, 89.3, 97.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1236 8.00 N 1038 7.00 C 4053 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=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 944.1 milliseconds 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 12 sheets defined 34.0% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 Processing helix chain 'A' and resid 23 through 28 removed outlier: 3.712A pdb=" N ALA A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 45 through 52 removed outlier: 3.625A pdb=" N GLU A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 69 removed outlier: 3.954A pdb=" N HIS A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 73 through 85 removed outlier: 4.233A pdb=" N ALA A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.964A pdb=" N ASN A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 215 " --> pdb=" O MET A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 219 through 223 removed outlier: 3.677A pdb=" N ARG A 223 " --> pdb=" O PRO A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 281 removed outlier: 4.203A pdb=" N ILE A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 16 removed outlier: 3.588A pdb=" N LEU B 13 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 28 removed outlier: 3.941A pdb=" N LEU B 26 " --> pdb=" O GLY B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 43 Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 62 through 69 removed outlier: 4.290A pdb=" N HIS B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 removed outlier: 4.108A pdb=" N ALA B 79 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 205 through 218 removed outlier: 3.597A pdb=" N ASN B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 270 through 281 removed outlier: 3.877A pdb=" N ASN B 274 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 281 " --> pdb=" O TYR B 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 16 removed outlier: 3.538A pdb=" N LYS C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 13 " --> pdb=" O ALA C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 27 Processing helix chain 'C' and resid 35 through 43 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.562A pdb=" N MET C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU C 53 " --> pdb=" O MET C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.896A pdb=" N HIS C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 72 Processing helix chain 'C' and resid 73 through 85 removed outlier: 3.823A pdb=" N PHE C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 205 through 218 removed outlier: 3.789A pdb=" N ASN C 213 " --> pdb=" O THR C 209 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 269 through 281 removed outlier: 4.246A pdb=" N ILE C 273 " --> pdb=" O GLU C 269 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN C 274 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR C 281 " --> pdb=" O TYR C 277 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 96 removed outlier: 7.151A pdb=" N LYS A 161 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 10.510A pdb=" N ASN A 151 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 11.004A pdb=" N THR A 159 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 181 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 239 " --> pdb=" O THR A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 105 Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 119 removed outlier: 6.356A pdb=" N THR A 115 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLY A 126 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 117 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 200 Processing sheet with id=AA5, first strand: chain 'B' and resid 95 through 96 Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AA7, first strand: chain 'B' and resid 115 through 119 removed outlier: 6.363A pdb=" N THR B 115 " --> pdb=" O GLY B 126 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY B 126 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B 117 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 197 through 200 Processing sheet with id=AA9, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.539A pdb=" N SER C 142 " --> pdb=" O THR C 264 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AB2, first strand: chain 'C' and resid 115 through 119 removed outlier: 6.466A pdb=" N THR C 115 " --> pdb=" O GLY C 126 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY C 126 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL C 117 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 128 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 198 through 200 222 hydrogen bonds defined for protein. 588 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2020 1.34 - 1.46: 1406 1.46 - 1.58: 2985 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 6465 Sorted by residual: bond pdb=" C THR B 237 " pdb=" N VAL B 238 " ideal model delta sigma weight residual 1.329 1.359 -0.030 1.32e-02 5.74e+03 5.24e+00 bond pdb=" C GLY B 228 " pdb=" N LEU B 229 " ideal model delta sigma weight residual 1.330 1.312 0.018 1.32e-02 5.74e+03 1.92e+00 bond pdb=" C LEU B 229 " pdb=" N TYR B 230 " ideal model delta sigma weight residual 1.331 1.313 0.019 1.38e-02 5.25e+03 1.81e+00 bond pdb=" C VAL B 238 " pdb=" N THR B 239 " ideal model delta sigma weight residual 1.330 1.349 -0.019 1.40e-02 5.10e+03 1.78e+00 bond pdb=" C ILE A 197 " pdb=" N LYS A 198 " ideal model delta sigma weight residual 1.330 1.341 -0.011 1.26e-02 6.30e+03 7.07e-01 ... (remaining 6460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 8734 1.88 - 3.76: 78 3.76 - 5.65: 2 5.65 - 7.53: 2 7.53 - 9.41: 1 Bond angle restraints: 8817 Sorted by residual: angle pdb=" C VAL B 227 " pdb=" N GLY B 228 " pdb=" CA GLY B 228 " ideal model delta sigma weight residual 122.33 120.11 2.22 7.30e-01 1.88e+00 9.28e+00 angle pdb=" CA LEU A 282 " pdb=" CB LEU A 282 " pdb=" CG LEU A 282 " ideal model delta sigma weight residual 116.30 125.71 -9.41 3.50e+00 8.16e-02 7.23e+00 angle pdb=" CA LEU B 125 " pdb=" CB LEU B 125 " pdb=" CG LEU B 125 " ideal model delta sigma weight residual 116.30 123.62 -7.32 3.50e+00 8.16e-02 4.38e+00 angle pdb=" N GLY B 228 " pdb=" CA GLY B 228 " pdb=" C GLY B 228 " ideal model delta sigma weight residual 111.04 114.60 -3.56 1.77e+00 3.19e-01 4.05e+00 angle pdb=" C MET B 196 " pdb=" N ILE B 197 " pdb=" CA ILE B 197 " ideal model delta sigma weight residual 122.91 120.35 2.56 1.43e+00 4.89e-01 3.21e+00 ... (remaining 8812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.69: 3650 14.69 - 29.39: 194 29.39 - 44.08: 39 44.08 - 58.77: 15 58.77 - 73.47: 2 Dihedral angle restraints: 3900 sinusoidal: 1449 harmonic: 2451 Sorted by residual: dihedral pdb=" CA TYR C 137 " pdb=" C TYR C 137 " pdb=" N SER C 138 " pdb=" CA SER C 138 " ideal model delta harmonic sigma weight residual 180.00 162.39 17.61 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA LEU A 279 " pdb=" C LEU A 279 " pdb=" N SER A 280 " pdb=" CA SER A 280 " ideal model delta harmonic sigma weight residual -180.00 -163.31 -16.69 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA SER B 138 " pdb=" C SER B 138 " pdb=" N ASN B 139 " pdb=" CA ASN B 139 " ideal model delta harmonic sigma weight residual -180.00 -164.02 -15.98 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 3897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 777 0.033 - 0.065: 215 0.065 - 0.098: 79 0.098 - 0.130: 36 0.130 - 0.163: 3 Chirality restraints: 1110 Sorted by residual: chirality pdb=" CG LEU A 282 " pdb=" CB LEU A 282 " pdb=" CD1 LEU A 282 " pdb=" CD2 LEU A 282 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CG LEU B 125 " pdb=" CB LEU B 125 " pdb=" CD1 LEU B 125 " pdb=" CD2 LEU B 125 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ILE A 252 " pdb=" N ILE A 252 " pdb=" C ILE A 252 " pdb=" CB ILE A 252 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1107 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 58 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO C 59 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 59 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 59 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 187 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO B 188 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 188 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 188 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 252 " 0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO C 253 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 253 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 253 " 0.014 5.00e-02 4.00e+02 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1165 2.76 - 3.30: 6745 3.30 - 3.83: 10484 3.83 - 4.37: 12270 4.37 - 4.90: 20879 Nonbonded interactions: 51543 Sorted by model distance: nonbonded pdb=" O GLY C 22 " pdb=" OG1 THR C 25 " model vdw 2.227 3.040 nonbonded pdb=" OG SER C 171 " pdb=" OG SER C 175 " model vdw 2.228 3.040 nonbonded pdb=" O PRO C 253 " pdb=" OG1 THR C 256 " model vdw 2.230 3.040 nonbonded pdb=" OG SER A 207 " pdb=" O LEU A 229 " model vdw 2.242 3.040 nonbonded pdb=" OG SER A 35 " pdb=" O SER C 30 " model vdw 2.250 3.040 ... (remaining 51538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.400 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.510 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 : 0.003 0.030 6465 Z= 0.173 Angle : 0.531 9.410 8817 Z= 0.303 Chirality : 0.039 0.163 1110 Planarity : 0.004 0.038 1095 Dihedral : 10.427 73.466 2316 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.41 % Allowed : 10.19 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.28), residues: 834 helix: 0.07 (0.37), residues: 201 sheet: 0.23 (0.43), residues: 114 loop : 0.78 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 192 HIS 0.002 0.001 HIS C 127 PHE 0.013 0.001 PHE A 50 TYR 0.006 0.001 TYR B 148 ARG 0.004 0.000 ARG C 223 Details of bonding type rmsd hydrogen bonds : bond 0.27479 ( 222) hydrogen bonds : angle 8.41456 ( 588) covalent geometry : bond 0.00350 ( 6465) covalent geometry : angle 0.53117 ( 8817) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 216 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9140 (ttmm) cc_final: 0.8839 (tttt) REVERT: A 84 MET cc_start: 0.8695 (tpt) cc_final: 0.8417 (tpt) REVERT: A 99 MET cc_start: 0.8190 (mmm) cc_final: 0.7716 (mmm) REVERT: A 101 MET cc_start: 0.8431 (mtp) cc_final: 0.7599 (mtp) REVERT: A 167 ILE cc_start: 0.9317 (pt) cc_final: 0.9085 (pt) REVERT: A 182 TYR cc_start: 0.7773 (p90) cc_final: 0.6865 (p90) REVERT: A 243 SER cc_start: 0.8655 (m) cc_final: 0.8449 (t) REVERT: B 8 ARG cc_start: 0.8582 (ttt-90) cc_final: 0.7786 (ttt180) REVERT: B 73 ASP cc_start: 0.8843 (t70) cc_final: 0.8328 (t0) REVERT: B 84 MET cc_start: 0.8752 (tpt) cc_final: 0.8357 (tpp) REVERT: B 232 ASP cc_start: 0.6519 (t0) cc_final: 0.6136 (t0) REVERT: B 269 GLU cc_start: 0.9031 (mp0) cc_final: 0.8821 (mp0) REVERT: C 33 LYS cc_start: 0.8206 (mttp) cc_final: 0.7974 (mmtp) REVERT: C 84 MET cc_start: 0.8550 (tpt) cc_final: 0.8266 (tpp) REVERT: C 98 ARG cc_start: 0.8578 (mtm110) cc_final: 0.7793 (mtm180) REVERT: C 148 TYR cc_start: 0.7659 (t80) cc_final: 0.7222 (t80) REVERT: C 150 TYR cc_start: 0.7908 (t80) cc_final: 0.7697 (t80) outliers start: 3 outliers final: 1 residues processed: 218 average time/residue: 0.2115 time to fit residues: 58.7360 Evaluate side-chains 144 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 0.0040 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 HIS A 94 ASN ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN A 195 ASN A 216 ASN B 68 HIS B 102 GLN B 111 ASN C 94 ASN C 151 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.098566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.082480 restraints weight = 19617.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.084940 restraints weight = 10482.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.086643 restraints weight = 7004.447| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6465 Z= 0.123 Angle : 0.594 9.056 8817 Z= 0.311 Chirality : 0.042 0.161 1110 Planarity : 0.004 0.040 1095 Dihedral : 4.608 35.483 889 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.13 % Allowed : 16.53 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.64 (0.28), residues: 834 helix: 0.21 (0.34), residues: 207 sheet: -0.09 (0.40), residues: 126 loop : 0.86 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 80 HIS 0.011 0.003 HIS B 68 PHE 0.013 0.002 PHE A 50 TYR 0.020 0.002 TYR B 148 ARG 0.007 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 222) hydrogen bonds : angle 5.75483 ( 588) covalent geometry : bond 0.00266 ( 6465) covalent geometry : angle 0.59436 ( 8817) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.727 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: A 73 ASP cc_start: 0.8421 (t70) cc_final: 0.8048 (t0) REVERT: A 84 MET cc_start: 0.8792 (tpt) cc_final: 0.8574 (tpt) REVERT: A 150 TYR cc_start: 0.7205 (t80) cc_final: 0.6868 (t80) REVERT: A 182 TYR cc_start: 0.7657 (p90) cc_final: 0.6821 (p90) REVERT: A 243 SER cc_start: 0.8600 (m) cc_final: 0.8333 (t) REVERT: B 8 ARG cc_start: 0.8510 (ttt-90) cc_final: 0.7878 (ttt180) REVERT: B 19 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7344 (ptt-90) REVERT: B 41 LYS cc_start: 0.9093 (ttmt) cc_final: 0.8675 (tttt) REVERT: B 73 ASP cc_start: 0.8507 (t70) cc_final: 0.7976 (t0) REVERT: B 84 MET cc_start: 0.8878 (tpt) cc_final: 0.8530 (tpp) REVERT: B 98 ARG cc_start: 0.8558 (mtm180) cc_final: 0.8266 (mtm180) REVERT: B 167 ILE cc_start: 0.9264 (pt) cc_final: 0.8909 (pt) REVERT: C 84 MET cc_start: 0.8921 (tpt) cc_final: 0.8676 (tpp) REVERT: C 98 ARG cc_start: 0.8651 (mtm110) cc_final: 0.8317 (mtm110) REVERT: C 148 TYR cc_start: 0.7721 (t80) cc_final: 0.7180 (t80) outliers start: 30 outliers final: 21 residues processed: 187 average time/residue: 0.2061 time to fit residues: 50.1395 Evaluate side-chains 174 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 76 optimal weight: 0.0040 chunk 21 optimal weight: 8.9990 overall best weight: 4.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 HIS A 87 GLN A 94 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 GLN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.094844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.079001 restraints weight = 19877.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.081332 restraints weight = 10489.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.082950 restraints weight = 6974.328| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6465 Z= 0.203 Angle : 0.622 7.122 8817 Z= 0.325 Chirality : 0.042 0.168 1110 Planarity : 0.004 0.046 1095 Dihedral : 4.838 28.282 889 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 6.47 % Allowed : 17.91 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.28), residues: 834 helix: 0.23 (0.35), residues: 207 sheet: -0.54 (0.39), residues: 138 loop : 0.76 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 80 HIS 0.007 0.002 HIS A 68 PHE 0.021 0.003 PHE A 166 TYR 0.016 0.002 TYR A 103 ARG 0.009 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 222) hydrogen bonds : angle 5.57439 ( 588) covalent geometry : bond 0.00450 ( 6465) covalent geometry : angle 0.62203 ( 8817) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8019 (mtm110) cc_final: 0.7609 (ptt-90) REVERT: A 73 ASP cc_start: 0.8290 (t70) cc_final: 0.8090 (t0) REVERT: A 84 MET cc_start: 0.8878 (tpt) cc_final: 0.8657 (tpt) REVERT: A 166 PHE cc_start: 0.9232 (t80) cc_final: 0.8995 (t80) REVERT: A 182 TYR cc_start: 0.7638 (p90) cc_final: 0.6778 (p90) REVERT: A 243 SER cc_start: 0.8671 (m) cc_final: 0.8426 (t) REVERT: B 8 ARG cc_start: 0.8485 (ttt-90) cc_final: 0.7847 (ttt180) REVERT: B 19 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7243 (ptt-90) REVERT: B 73 ASP cc_start: 0.8668 (t70) cc_final: 0.8117 (t0) REVERT: B 84 MET cc_start: 0.8868 (tpt) cc_final: 0.8544 (tpp) REVERT: B 98 ARG cc_start: 0.8617 (mtm180) cc_final: 0.8267 (mtm180) REVERT: B 230 TYR cc_start: 0.8134 (t80) cc_final: 0.7845 (t80) REVERT: C 84 MET cc_start: 0.8894 (tpt) cc_final: 0.8643 (tpp) REVERT: C 90 MET cc_start: 0.8729 (mmm) cc_final: 0.8487 (mmm) REVERT: C 98 ARG cc_start: 0.8640 (mtm110) cc_final: 0.8236 (mtm110) REVERT: C 148 TYR cc_start: 0.7789 (t80) cc_final: 0.7241 (t80) outliers start: 47 outliers final: 34 residues processed: 187 average time/residue: 0.1928 time to fit residues: 47.1654 Evaluate side-chains 182 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 251 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 25 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 GLN A 94 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.095008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.079025 restraints weight = 19951.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.081419 restraints weight = 10400.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.082969 restraints weight = 6859.070| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6465 Z= 0.178 Angle : 0.597 7.059 8817 Z= 0.314 Chirality : 0.042 0.128 1110 Planarity : 0.004 0.045 1095 Dihedral : 4.769 22.318 888 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 7.16 % Allowed : 19.83 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.26 (0.28), residues: 834 helix: 0.01 (0.35), residues: 207 sheet: -0.59 (0.40), residues: 138 loop : 0.68 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 80 HIS 0.004 0.001 HIS B 127 PHE 0.027 0.002 PHE B 166 TYR 0.020 0.002 TYR A 103 ARG 0.010 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 222) hydrogen bonds : angle 5.38885 ( 588) covalent geometry : bond 0.00395 ( 6465) covalent geometry : angle 0.59654 ( 8817) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 158 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8116 (mtm110) cc_final: 0.7748 (ptt-90) REVERT: A 84 MET cc_start: 0.8916 (tpt) cc_final: 0.8705 (tpt) REVERT: A 166 PHE cc_start: 0.9177 (t80) cc_final: 0.8879 (t80) REVERT: A 182 TYR cc_start: 0.7614 (p90) cc_final: 0.6797 (p90) REVERT: A 211 MET cc_start: 0.8665 (mpp) cc_final: 0.8388 (mpp) REVERT: A 243 SER cc_start: 0.8701 (m) cc_final: 0.8447 (t) REVERT: B 8 ARG cc_start: 0.8441 (ttt-90) cc_final: 0.7817 (ttt180) REVERT: B 19 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7307 (ptt-90) REVERT: B 41 LYS cc_start: 0.9090 (ttmt) cc_final: 0.8870 (tppt) REVERT: B 73 ASP cc_start: 0.8676 (t70) cc_final: 0.8068 (t0) REVERT: B 196 MET cc_start: 0.7490 (mmp) cc_final: 0.7238 (mmp) REVERT: B 230 TYR cc_start: 0.8118 (t80) cc_final: 0.7751 (t80) REVERT: B 269 GLU cc_start: 0.9030 (mp0) cc_final: 0.8745 (mp0) REVERT: C 84 MET cc_start: 0.8895 (tpt) cc_final: 0.8625 (tpp) REVERT: C 90 MET cc_start: 0.8766 (mmm) cc_final: 0.7951 (mmp) REVERT: C 93 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8302 (p0) REVERT: C 98 ARG cc_start: 0.8668 (mtm110) cc_final: 0.8205 (mtm180) REVERT: C 125 LEU cc_start: 0.9178 (pp) cc_final: 0.8913 (pt) REVERT: C 148 TYR cc_start: 0.7775 (t80) cc_final: 0.7155 (t80) REVERT: C 236 VAL cc_start: 0.7997 (OUTLIER) cc_final: 0.7747 (t) outliers start: 52 outliers final: 32 residues processed: 194 average time/residue: 0.2212 time to fit residues: 57.1232 Evaluate side-chains 183 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 236 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 4.9990 chunk 67 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 94 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.093385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.077267 restraints weight = 20211.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.079466 restraints weight = 10551.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.080993 restraints weight = 7183.640| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 6465 Z= 0.253 Angle : 0.666 8.634 8817 Z= 0.351 Chirality : 0.043 0.142 1110 Planarity : 0.004 0.047 1095 Dihedral : 5.164 25.473 888 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 8.13 % Allowed : 20.11 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.28), residues: 834 helix: -0.30 (0.35), residues: 207 sheet: -0.99 (0.41), residues: 120 loop : 0.41 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 80 HIS 0.005 0.002 HIS B 127 PHE 0.023 0.003 PHE C 166 TYR 0.023 0.002 TYR A 103 ARG 0.012 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 222) hydrogen bonds : angle 5.58408 ( 588) covalent geometry : bond 0.00557 ( 6465) covalent geometry : angle 0.66571 ( 8817) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 153 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8288 (tp) REVERT: A 19 ARG cc_start: 0.8095 (mtm110) cc_final: 0.7729 (ptt-90) REVERT: A 87 GLN cc_start: 0.8591 (tp-100) cc_final: 0.8141 (tm-30) REVERT: A 182 TYR cc_start: 0.7643 (p90) cc_final: 0.6829 (p90) REVERT: A 211 MET cc_start: 0.8738 (mpp) cc_final: 0.8465 (mpp) REVERT: A 243 SER cc_start: 0.8678 (m) cc_final: 0.8451 (t) REVERT: B 8 ARG cc_start: 0.8413 (ttt-90) cc_final: 0.7844 (ttt180) REVERT: B 19 ARG cc_start: 0.7881 (mtm-85) cc_final: 0.7326 (ptt-90) REVERT: B 41 LYS cc_start: 0.9065 (ttmt) cc_final: 0.8789 (tppt) REVERT: B 73 ASP cc_start: 0.8712 (t70) cc_final: 0.8242 (t0) REVERT: B 76 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8550 (ptp-110) REVERT: B 196 MET cc_start: 0.7500 (mmp) cc_final: 0.7278 (tpt) REVERT: B 230 TYR cc_start: 0.8181 (t80) cc_final: 0.7853 (t80) REVERT: C 148 TYR cc_start: 0.7635 (t80) cc_final: 0.7093 (t80) REVERT: C 236 VAL cc_start: 0.8101 (OUTLIER) cc_final: 0.7896 (t) outliers start: 59 outliers final: 44 residues processed: 198 average time/residue: 0.2347 time to fit residues: 63.1642 Evaluate side-chains 190 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 259 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 50 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 ASN ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.094348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.078242 restraints weight = 20106.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.080517 restraints weight = 10604.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.082093 restraints weight = 7165.663| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6465 Z= 0.192 Angle : 0.645 9.779 8817 Z= 0.335 Chirality : 0.042 0.135 1110 Planarity : 0.004 0.046 1095 Dihedral : 5.057 25.108 888 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 7.85 % Allowed : 21.63 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.28), residues: 834 helix: -0.31 (0.34), residues: 207 sheet: -1.04 (0.40), residues: 138 loop : 0.46 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 80 HIS 0.005 0.002 HIS B 127 PHE 0.022 0.002 PHE C 166 TYR 0.022 0.002 TYR A 103 ARG 0.013 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 222) hydrogen bonds : angle 5.42186 ( 588) covalent geometry : bond 0.00429 ( 6465) covalent geometry : angle 0.64533 ( 8817) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 152 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8308 (tp) REVERT: A 19 ARG cc_start: 0.8112 (mtm110) cc_final: 0.7751 (ptt-90) REVERT: A 182 TYR cc_start: 0.7628 (p90) cc_final: 0.6856 (p90) REVERT: A 211 MET cc_start: 0.8788 (mpp) cc_final: 0.8447 (mpp) REVERT: A 243 SER cc_start: 0.8661 (m) cc_final: 0.8431 (t) REVERT: B 8 ARG cc_start: 0.8354 (ttt-90) cc_final: 0.7779 (ttt180) REVERT: B 19 ARG cc_start: 0.7953 (mtm-85) cc_final: 0.7379 (ptt-90) REVERT: B 41 LYS cc_start: 0.9075 (ttmt) cc_final: 0.8863 (tppt) REVERT: B 73 ASP cc_start: 0.8615 (t70) cc_final: 0.8121 (t0) REVERT: B 76 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8529 (ptp-110) REVERT: B 230 TYR cc_start: 0.8174 (t80) cc_final: 0.7859 (t80) REVERT: C 87 GLN cc_start: 0.8182 (tt0) cc_final: 0.7776 (tt0) REVERT: C 148 TYR cc_start: 0.7570 (t80) cc_final: 0.7043 (t80) REVERT: C 236 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7863 (t) outliers start: 57 outliers final: 52 residues processed: 192 average time/residue: 0.1707 time to fit residues: 43.3450 Evaluate side-chains 197 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 142 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 259 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 ASN ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.097111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.081078 restraints weight = 19891.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.083462 restraints weight = 10419.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.085088 restraints weight = 6937.578| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6465 Z= 0.114 Angle : 0.630 10.115 8817 Z= 0.318 Chirality : 0.041 0.187 1110 Planarity : 0.004 0.042 1095 Dihedral : 4.631 22.434 888 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 5.79 % Allowed : 24.79 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.28), residues: 834 helix: -0.27 (0.34), residues: 213 sheet: -0.35 (0.44), residues: 120 loop : 0.45 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 80 HIS 0.003 0.001 HIS B 127 PHE 0.014 0.002 PHE A 50 TYR 0.022 0.002 TYR A 103 ARG 0.014 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 222) hydrogen bonds : angle 5.05814 ( 588) covalent geometry : bond 0.00260 ( 6465) covalent geometry : angle 0.62953 ( 8817) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8072 (mtm110) cc_final: 0.7819 (ptt-90) REVERT: A 87 GLN cc_start: 0.8609 (tp-100) cc_final: 0.8354 (tm-30) REVERT: A 182 TYR cc_start: 0.7550 (p90) cc_final: 0.6824 (p90) REVERT: A 211 MET cc_start: 0.8828 (mpp) cc_final: 0.8486 (mpp) REVERT: A 243 SER cc_start: 0.8640 (m) cc_final: 0.8377 (t) REVERT: B 8 ARG cc_start: 0.8268 (ttt-90) cc_final: 0.7719 (ttt180) REVERT: B 19 ARG cc_start: 0.7945 (mtm-85) cc_final: 0.7342 (ptt-90) REVERT: B 41 LYS cc_start: 0.9098 (ttmt) cc_final: 0.8887 (tppt) REVERT: B 73 ASP cc_start: 0.8483 (t70) cc_final: 0.7941 (t0) REVERT: B 230 TYR cc_start: 0.8181 (t80) cc_final: 0.7872 (t80) REVERT: C 90 MET cc_start: 0.8938 (mmm) cc_final: 0.8736 (mmp) REVERT: C 98 ARG cc_start: 0.8749 (mtm110) cc_final: 0.8152 (mtm180) REVERT: C 125 LEU cc_start: 0.9066 (pp) cc_final: 0.8784 (pt) REVERT: C 148 TYR cc_start: 0.7550 (t80) cc_final: 0.6984 (t80) REVERT: C 236 VAL cc_start: 0.8017 (OUTLIER) cc_final: 0.7737 (t) outliers start: 42 outliers final: 33 residues processed: 188 average time/residue: 0.1799 time to fit residues: 44.8466 Evaluate side-chains 184 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 259 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 13 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 78 optimal weight: 0.0020 chunk 0 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 HIS ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.095184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.079105 restraints weight = 20082.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.081433 restraints weight = 10562.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.082992 restraints weight = 7141.012| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6465 Z= 0.176 Angle : 0.665 11.848 8817 Z= 0.334 Chirality : 0.042 0.177 1110 Planarity : 0.004 0.042 1095 Dihedral : 4.819 24.538 888 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 6.75 % Allowed : 24.38 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.29), residues: 834 helix: -0.23 (0.35), residues: 207 sheet: -0.85 (0.41), residues: 138 loop : 0.50 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 80 HIS 0.004 0.001 HIS B 127 PHE 0.028 0.002 PHE C 166 TYR 0.026 0.002 TYR C 150 ARG 0.009 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 222) hydrogen bonds : angle 5.23068 ( 588) covalent geometry : bond 0.00392 ( 6465) covalent geometry : angle 0.66536 ( 8817) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 154 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8118 (mtm110) cc_final: 0.7783 (ptt-90) REVERT: A 182 TYR cc_start: 0.7515 (p90) cc_final: 0.6827 (p90) REVERT: A 211 MET cc_start: 0.8881 (mpp) cc_final: 0.8522 (mpp) REVERT: A 243 SER cc_start: 0.8662 (m) cc_final: 0.8419 (t) REVERT: B 8 ARG cc_start: 0.8291 (ttt-90) cc_final: 0.7798 (ttt180) REVERT: B 19 ARG cc_start: 0.7983 (mtm-85) cc_final: 0.7561 (ptt-90) REVERT: B 73 ASP cc_start: 0.8592 (t70) cc_final: 0.8113 (t0) REVERT: B 76 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8520 (ptp-110) REVERT: B 87 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8150 (tm-30) REVERT: B 230 TYR cc_start: 0.8173 (t80) cc_final: 0.7876 (t80) REVERT: B 266 GLN cc_start: 0.8656 (mt0) cc_final: 0.8369 (mt0) REVERT: B 269 GLU cc_start: 0.9029 (mp0) cc_final: 0.8670 (mp0) REVERT: C 98 ARG cc_start: 0.8726 (mtm110) cc_final: 0.8075 (mtm180) REVERT: C 125 LEU cc_start: 0.9138 (pp) cc_final: 0.8848 (pt) REVERT: C 148 TYR cc_start: 0.7558 (t80) cc_final: 0.7022 (t80) REVERT: C 236 VAL cc_start: 0.8080 (OUTLIER) cc_final: 0.7806 (t) outliers start: 49 outliers final: 42 residues processed: 187 average time/residue: 0.1876 time to fit residues: 46.5364 Evaluate side-chains 192 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 259 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.096223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.080159 restraints weight = 19999.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.082587 restraints weight = 10443.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.084103 restraints weight = 6967.108| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6465 Z= 0.136 Angle : 0.677 13.215 8817 Z= 0.334 Chirality : 0.042 0.149 1110 Planarity : 0.004 0.042 1095 Dihedral : 4.719 23.699 888 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 6.89 % Allowed : 24.24 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.01 (0.29), residues: 834 helix: -0.22 (0.35), residues: 207 sheet: -1.03 (0.39), residues: 159 loop : 0.69 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 80 HIS 0.004 0.001 HIS B 127 PHE 0.028 0.002 PHE C 166 TYR 0.024 0.002 TYR B 148 ARG 0.009 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 222) hydrogen bonds : angle 5.12150 ( 588) covalent geometry : bond 0.00311 ( 6465) covalent geometry : angle 0.67729 ( 8817) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 157 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8279 (tp) REVERT: A 19 ARG cc_start: 0.8080 (mtm110) cc_final: 0.7748 (ptt-90) REVERT: A 182 TYR cc_start: 0.7546 (p90) cc_final: 0.6840 (p90) REVERT: A 211 MET cc_start: 0.8864 (mpp) cc_final: 0.8492 (mpp) REVERT: A 243 SER cc_start: 0.8685 (m) cc_final: 0.8420 (t) REVERT: B 8 ARG cc_start: 0.8250 (ttt-90) cc_final: 0.7718 (ttt180) REVERT: B 19 ARG cc_start: 0.8024 (mtm-85) cc_final: 0.7581 (ptt-90) REVERT: B 73 ASP cc_start: 0.8560 (t70) cc_final: 0.7982 (t0) REVERT: B 76 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8429 (ptp-110) REVERT: B 87 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8235 (tm-30) REVERT: B 230 TYR cc_start: 0.8243 (t80) cc_final: 0.7933 (t80) REVERT: C 93 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8478 (p0) REVERT: C 98 ARG cc_start: 0.8708 (mtm110) cc_final: 0.8023 (mtm180) REVERT: C 125 LEU cc_start: 0.9090 (pp) cc_final: 0.8841 (pt) REVERT: C 148 TYR cc_start: 0.7543 (t80) cc_final: 0.7016 (t80) REVERT: C 236 VAL cc_start: 0.8005 (OUTLIER) cc_final: 0.7600 (t) outliers start: 50 outliers final: 39 residues processed: 193 average time/residue: 0.1896 time to fit residues: 49.5701 Evaluate side-chains 191 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 259 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.096020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.080084 restraints weight = 19843.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.082424 restraints weight = 10393.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.084036 restraints weight = 6946.466| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6465 Z= 0.153 Angle : 0.699 13.178 8817 Z= 0.346 Chirality : 0.042 0.175 1110 Planarity : 0.004 0.042 1095 Dihedral : 4.740 23.932 888 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 6.61 % Allowed : 24.10 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.01 (0.29), residues: 834 helix: -0.29 (0.35), residues: 207 sheet: -0.96 (0.40), residues: 159 loop : 0.73 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 80 HIS 0.004 0.002 HIS B 127 PHE 0.030 0.002 PHE C 166 TYR 0.026 0.002 TYR C 150 ARG 0.011 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 222) hydrogen bonds : angle 5.14906 ( 588) covalent geometry : bond 0.00348 ( 6465) covalent geometry : angle 0.69864 ( 8817) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8279 (tp) REVERT: A 19 ARG cc_start: 0.8193 (mtm110) cc_final: 0.7809 (ptt-90) REVERT: A 182 TYR cc_start: 0.7515 (p90) cc_final: 0.6844 (p90) REVERT: A 211 MET cc_start: 0.8874 (mpp) cc_final: 0.8520 (mpp) REVERT: A 243 SER cc_start: 0.8675 (m) cc_final: 0.8420 (t) REVERT: B 8 ARG cc_start: 0.8253 (ttt-90) cc_final: 0.7780 (ttt180) REVERT: B 19 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7573 (ptt-90) REVERT: B 73 ASP cc_start: 0.8589 (t70) cc_final: 0.8024 (t0) REVERT: B 76 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8497 (ptp-110) REVERT: B 87 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8243 (tm-30) REVERT: B 196 MET cc_start: 0.7360 (tpt) cc_final: 0.7148 (tpt) REVERT: B 230 TYR cc_start: 0.8333 (t80) cc_final: 0.8006 (t80) REVERT: C 93 ASN cc_start: 0.8974 (OUTLIER) cc_final: 0.8452 (p0) REVERT: C 98 ARG cc_start: 0.8723 (mtm110) cc_final: 0.8019 (mtm180) REVERT: C 125 LEU cc_start: 0.9104 (pp) cc_final: 0.8867 (pt) REVERT: C 148 TYR cc_start: 0.7547 (t80) cc_final: 0.7036 (t80) REVERT: C 236 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7547 (t) outliers start: 48 outliers final: 40 residues processed: 192 average time/residue: 0.1870 time to fit residues: 47.3613 Evaluate side-chains 198 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 259 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 22 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 68 optimal weight: 0.0000 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 overall best weight: 2.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.096431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.080472 restraints weight = 20301.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.082965 restraints weight = 10465.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.084578 restraints weight = 6913.643| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6465 Z= 0.135 Angle : 0.711 13.573 8817 Z= 0.349 Chirality : 0.042 0.144 1110 Planarity : 0.004 0.041 1095 Dihedral : 4.687 23.530 888 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 6.34 % Allowed : 24.79 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.30), residues: 834 helix: -0.33 (0.34), residues: 213 sheet: -0.93 (0.40), residues: 159 loop : 0.83 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 80 HIS 0.004 0.001 HIS B 127 PHE 0.031 0.002 PHE C 166 TYR 0.022 0.002 TYR B 103 ARG 0.009 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 222) hydrogen bonds : angle 5.06246 ( 588) covalent geometry : bond 0.00311 ( 6465) covalent geometry : angle 0.71093 ( 8817) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2603.97 seconds wall clock time: 48 minutes 1.55 seconds (2881.55 seconds total)