Starting phenix.real_space_refine on Fri Oct 10 13:44:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k44_36872/10_2025/8k44_36872.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k44_36872/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8k44_36872/10_2025/8k44_36872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k44_36872/10_2025/8k44_36872.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k44_36872/10_2025/8k44_36872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k44_36872/10_2025/8k44_36872.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.91, per 1000 atoms: 0.30 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: 0.65 Conformation dependent library (CDL) restraints added in 472.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.26 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: 0.90 Time building geometry restraints manager: 0.78 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: 0.01 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: 0.460 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.490 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.930 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG C 223 TYR 0.006 0.001 TYR B 148 PHE 0.013 0.001 PHE A 50 TRP 0.005 0.001 TRP A 192 HIS 0.002 0.001 HIS C 127 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6465) covalent geometry : angle 0.53117 ( 8817) hydrogen bonds : bond 0.27479 ( 222) hydrogen bonds : angle 8.41456 ( 588) *********************** 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 : 0.241 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: 0.8815 (tttt) REVERT: A 84 MET cc_start: 0.8695 (tpt) cc_final: 0.8415 (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: 0.7597 (mtp) REVERT: A 167 ILE cc_start: 0.9317 (pt) cc_final: 0.9086 (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: 0.8448 (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: 0.8329 (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: 0.6135 (t0) REVERT: B 269 GLU cc_start: 0.9031 (mp0) cc_final: 0.8817 (mp0) REVERT: C 33 LYS cc_start: 0.8206 (mttp) cc_final: 0.7977 (mmtp) REVERT: C 84 MET cc_start: 0.8550 (tpt) cc_final: 0.8265 (tpp) REVERT: C 98 ARG cc_start: 0.8578 (mtm110) cc_final: 0.7792 (mtm180) REVERT: C 148 TYR cc_start: 0.7659 (t80) cc_final: 0.7223 (t80) REVERT: C 150 TYR cc_start: 0.7908 (t80) cc_final: 0.7696 (t80) outliers start: 3 outliers final: 1 residues processed: 218 average time/residue: 0.0921 time to fit residues: 25.5784 Evaluate side-chains 145 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 0.0040 overall best weight: 3.1998 ------------------------------------------------------------------------------- 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 191 ASN A 195 ASN A 216 ASN B 68 HIS B 102 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.096260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.079966 restraints weight = 20161.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.082344 restraints weight = 10795.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.084047 restraints weight = 7260.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.085161 restraints weight = 5545.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.085810 restraints weight = 4637.594| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2288 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= 0.167 Angle : 0.616 9.469 8817 Z= 0.326 Chirality : 0.042 0.146 1110 Planarity : 0.004 0.044 1095 Dihedral : 4.856 34.582 889 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 5.51 % Allowed : 16.25 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.28), residues: 834 helix: 0.18 (0.35), residues: 207 sheet: -0.21 (0.40), residues: 126 loop : 0.79 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 19 TYR 0.014 0.002 TYR B 281 PHE 0.014 0.002 PHE A 50 TRP 0.008 0.001 TRP C 80 HIS 0.012 0.003 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 6465) covalent geometry : angle 0.61647 ( 8817) hydrogen bonds : bond 0.04667 ( 222) hydrogen bonds : angle 5.94236 ( 588) *********************** 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 201 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.275 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 41 LYS cc_start: 0.9222 (ttmm) cc_final: 0.8790 (tttt) REVERT: A 73 ASP cc_start: 0.8509 (t70) cc_final: 0.8134 (t0) REVERT: A 84 MET cc_start: 0.8833 (tpt) cc_final: 0.8615 (tpt) REVERT: A 182 TYR cc_start: 0.7611 (p90) cc_final: 0.6788 (p90) REVERT: A 243 SER cc_start: 0.8600 (m) cc_final: 0.8355 (t) REVERT: B 8 ARG cc_start: 0.8483 (ttt-90) cc_final: 0.7904 (ttt180) REVERT: B 19 ARG cc_start: 0.7887 (mtm-85) cc_final: 0.7371 (ptt-90) REVERT: B 41 LYS cc_start: 0.9042 (ttmt) cc_final: 0.8568 (tttp) REVERT: B 73 ASP cc_start: 0.8575 (t70) cc_final: 0.8012 (t0) REVERT: B 84 MET cc_start: 0.8927 (tpt) cc_final: 0.8617 (tpp) REVERT: B 167 ILE cc_start: 0.9295 (pt) cc_final: 0.8930 (pt) REVERT: C 84 MET cc_start: 0.8915 (tpt) cc_final: 0.8699 (tpp) REVERT: C 148 TYR cc_start: 0.7699 (t80) cc_final: 0.7193 (t80) REVERT: C 211 MET cc_start: 0.9007 (mtp) cc_final: 0.8713 (mtm) outliers start: 40 outliers final: 29 residues processed: 186 average time/residue: 0.0767 time to fit residues: 18.8308 Evaluate side-chains 173 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 VAL 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 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 272 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 68 HIS 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 B residue 252 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 251 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 6 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 chunk 49 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 overall best weight: 3.6586 ------------------------------------------------------------------------------- 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 B 68 HIS B 87 GLN B 111 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.095448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.079216 restraints weight = 19982.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.081538 restraints weight = 10727.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.083212 restraints weight = 7235.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.084062 restraints weight = 5541.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.084906 restraints weight = 4749.507| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6465 Z= 0.175 Angle : 0.598 7.069 8817 Z= 0.314 Chirality : 0.042 0.135 1110 Planarity : 0.004 0.047 1095 Dihedral : 4.839 26.610 889 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 6.75 % Allowed : 17.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.28), residues: 834 helix: 0.35 (0.36), residues: 207 sheet: -0.57 (0.39), residues: 138 loop : 0.73 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 19 TYR 0.019 0.002 TYR B 148 PHE 0.020 0.002 PHE B 166 TRP 0.005 0.001 TRP C 80 HIS 0.014 0.003 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 6465) covalent geometry : angle 0.59841 ( 8817) hydrogen bonds : bond 0.04146 ( 222) hydrogen bonds : angle 5.53582 ( 588) *********************** 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 203 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 154 time to evaluate : 0.199 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: A 19 ARG cc_start: 0.8016 (mtm110) cc_final: 0.7709 (ptt-90) REVERT: A 41 LYS cc_start: 0.9202 (ttmm) cc_final: 0.8859 (tttp) REVERT: A 84 MET cc_start: 0.8851 (tpt) cc_final: 0.8637 (tpt) REVERT: A 182 TYR cc_start: 0.7626 (p90) cc_final: 0.6809 (p90) REVERT: A 243 SER cc_start: 0.8613 (m) cc_final: 0.8394 (t) REVERT: B 8 ARG cc_start: 0.8452 (ttt-90) cc_final: 0.7840 (ttt180) REVERT: B 19 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7304 (ptt-90) REVERT: B 41 LYS cc_start: 0.9023 (ttmt) cc_final: 0.8614 (tttt) REVERT: B 73 ASP cc_start: 0.8584 (t70) cc_final: 0.8086 (t0) REVERT: B 84 MET cc_start: 0.8854 (tpt) cc_final: 0.8550 (tpp) REVERT: B 230 TYR cc_start: 0.8086 (t80) cc_final: 0.7778 (t80) REVERT: C 84 MET cc_start: 0.8853 (tpt) cc_final: 0.8615 (tpp) REVERT: C 90 MET cc_start: 0.8783 (mmm) cc_final: 0.8524 (mmp) REVERT: C 93 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.8302 (p0) REVERT: C 148 TYR cc_start: 0.7743 (t80) cc_final: 0.7196 (t80) outliers start: 49 outliers final: 37 residues processed: 184 average time/residue: 0.0819 time to fit residues: 19.7401 Evaluate side-chains 186 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU 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 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 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 261 SER Chi-restraints excluded: chain A residue 272 VAL 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 168 THR 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 252 ILE Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 61 ILE 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 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 45 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 38 optimal weight: 0.0050 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 87 GLN A 94 ASN C 191 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.097148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.081033 restraints weight = 19939.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.083416 restraints weight = 10572.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.084974 restraints weight = 7088.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.086076 restraints weight = 5479.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.086652 restraints weight = 4579.726| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3110 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= 0.114 Angle : 0.579 6.997 8817 Z= 0.299 Chirality : 0.041 0.142 1110 Planarity : 0.004 0.043 1095 Dihedral : 4.511 16.473 888 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 5.37 % Allowed : 21.49 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.28), residues: 834 helix: 0.37 (0.35), residues: 207 sheet: -0.53 (0.40), residues: 138 loop : 0.70 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 19 TYR 0.022 0.002 TYR A 103 PHE 0.030 0.002 PHE B 166 TRP 0.004 0.001 TRP C 80 HIS 0.003 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6465) covalent geometry : angle 0.57900 ( 8817) hydrogen bonds : bond 0.03453 ( 222) hydrogen bonds : angle 5.15433 ( 588) *********************** 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 205 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.238 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: 0.7949 (mtm110) cc_final: 0.7729 (ptt-90) REVERT: A 41 LYS cc_start: 0.9218 (ttmm) cc_final: 0.8845 (tttp) REVERT: A 52 GLU cc_start: 0.8588 (mm-30) cc_final: 0.7971 (mm-30) REVERT: A 95 VAL cc_start: 0.9620 (t) cc_final: 0.9419 (p) REVERT: A 166 PHE cc_start: 0.9041 (t80) cc_final: 0.8424 (t80) REVERT: A 182 TYR cc_start: 0.7628 (p90) cc_final: 0.6845 (p90) REVERT: A 243 SER cc_start: 0.8591 (m) cc_final: 0.8346 (t) REVERT: B 8 ARG cc_start: 0.8321 (ttt-90) cc_final: 0.7794 (ttt180) REVERT: B 19 ARG cc_start: 0.7817 (mtm-85) cc_final: 0.7247 (ptt-90) REVERT: B 73 ASP cc_start: 0.8495 (t70) cc_final: 0.7742 (t0) REVERT: B 84 MET cc_start: 0.8827 (tpt) cc_final: 0.8533 (tpp) REVERT: B 196 MET cc_start: 0.7361 (mmp) cc_final: 0.7085 (mmp) REVERT: C 84 MET cc_start: 0.8810 (tpt) cc_final: 0.8554 (tpp) REVERT: C 90 MET cc_start: 0.8713 (mmm) cc_final: 0.8070 (mmp) REVERT: C 93 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8396 (p0) REVERT: C 125 LEU cc_start: 0.9175 (pp) cc_final: 0.8938 (pt) REVERT: C 148 TYR cc_start: 0.7691 (t80) cc_final: 0.7128 (t80) REVERT: C 236 VAL cc_start: 0.8043 (OUTLIER) cc_final: 0.7791 (t) outliers start: 39 outliers final: 26 residues processed: 191 average time/residue: 0.0766 time to fit residues: 19.4258 Evaluate side-chains 179 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 45 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 55 GLN 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 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 93 ASN 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 190 GLU 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 12 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 87 GLN A 94 ASN A 191 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.096570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.080315 restraints weight = 20305.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.082748 restraints weight = 10716.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.084264 restraints weight = 7143.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.085396 restraints weight = 5539.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.086022 restraints weight = 4641.357| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6465 Z= 0.139 Angle : 0.588 7.094 8817 Z= 0.304 Chirality : 0.041 0.132 1110 Planarity : 0.004 0.042 1095 Dihedral : 4.575 19.794 888 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 6.34 % Allowed : 21.21 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.28), residues: 834 helix: 0.19 (0.35), residues: 213 sheet: -0.58 (0.40), residues: 138 loop : 0.70 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 19 TYR 0.021 0.002 TYR A 103 PHE 0.016 0.002 PHE A 145 TRP 0.004 0.001 TRP A 80 HIS 0.003 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6465) covalent geometry : angle 0.58846 ( 8817) hydrogen bonds : bond 0.03461 ( 222) hydrogen bonds : angle 5.03998 ( 588) *********************** 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 204 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7975 (mtm110) cc_final: 0.7751 (ptt-90) REVERT: A 41 LYS cc_start: 0.9218 (ttmm) cc_final: 0.8838 (tttp) REVERT: A 52 GLU cc_start: 0.8647 (mm-30) cc_final: 0.7944 (mm-30) REVERT: A 55 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8600 (pm20) REVERT: A 182 TYR cc_start: 0.7532 (p90) cc_final: 0.6858 (p90) REVERT: A 243 SER cc_start: 0.8584 (m) cc_final: 0.8338 (t) REVERT: B 8 ARG cc_start: 0.8293 (ttt-90) cc_final: 0.7825 (ttt180) REVERT: B 19 ARG cc_start: 0.7859 (mtm-85) cc_final: 0.7124 (ptt90) REVERT: B 73 ASP cc_start: 0.8522 (t70) cc_final: 0.7739 (t0) REVERT: B 196 MET cc_start: 0.7452 (mmp) cc_final: 0.7186 (mmp) REVERT: B 230 TYR cc_start: 0.8021 (t80) cc_final: 0.7702 (t80) REVERT: C 84 MET cc_start: 0.8794 (tpt) cc_final: 0.8530 (tpp) REVERT: C 90 MET cc_start: 0.8772 (mmm) cc_final: 0.8155 (mmp) REVERT: C 93 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8385 (p0) REVERT: C 98 ARG cc_start: 0.8738 (mtm110) cc_final: 0.8195 (mtm180) REVERT: C 148 TYR cc_start: 0.7569 (t80) cc_final: 0.7031 (t80) outliers start: 46 outliers final: 34 residues processed: 188 average time/residue: 0.0755 time to fit residues: 19.1837 Evaluate side-chains 186 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 45 THR 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 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 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 VAL 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 190 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 93 ASN 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 190 GLU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 219 VAL 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 2 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 87 GLN A 94 ASN A 216 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.095829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.079728 restraints weight = 20135.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.082031 restraints weight = 10651.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.083645 restraints weight = 7147.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.084701 restraints weight = 5526.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.085030 restraints weight = 4634.566| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6465 Z= 0.168 Angle : 0.602 7.036 8817 Z= 0.312 Chirality : 0.041 0.132 1110 Planarity : 0.004 0.042 1095 Dihedral : 4.701 22.619 888 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 6.75 % Allowed : 22.31 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.29), residues: 834 helix: 0.10 (0.35), residues: 213 sheet: -0.75 (0.40), residues: 144 loop : 0.72 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 19 TYR 0.020 0.002 TYR A 103 PHE 0.015 0.002 PHE A 50 TRP 0.005 0.001 TRP C 80 HIS 0.004 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 6465) covalent geometry : angle 0.60215 ( 8817) hydrogen bonds : bond 0.03498 ( 222) hydrogen bonds : angle 5.09627 ( 588) *********************** 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 205 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 156 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8283 (tp) REVERT: A 19 ARG cc_start: 0.8011 (mtm110) cc_final: 0.7741 (ptt-90) REVERT: A 41 LYS cc_start: 0.9220 (ttmm) cc_final: 0.8820 (tttp) REVERT: A 182 TYR cc_start: 0.7560 (p90) cc_final: 0.6893 (p90) REVERT: A 243 SER cc_start: 0.8613 (m) cc_final: 0.8361 (t) REVERT: B 8 ARG cc_start: 0.8288 (ttt-90) cc_final: 0.7755 (ttt180) REVERT: B 19 ARG cc_start: 0.7852 (mtm-85) cc_final: 0.7309 (ptt-90) REVERT: B 73 ASP cc_start: 0.8569 (t70) cc_final: 0.8035 (t0) REVERT: B 76 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8350 (ptp-110) REVERT: B 196 MET cc_start: 0.7467 (mmp) cc_final: 0.7252 (mmp) REVERT: C 84 MET cc_start: 0.8797 (tpt) cc_final: 0.8520 (tpp) REVERT: C 90 MET cc_start: 0.8809 (mmm) cc_final: 0.8063 (mmp) REVERT: C 93 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8309 (p0) REVERT: C 98 ARG cc_start: 0.8764 (mtm110) cc_final: 0.8237 (mtm180) REVERT: C 148 TYR cc_start: 0.7579 (t80) cc_final: 0.6981 (t80) outliers start: 49 outliers final: 38 residues processed: 185 average time/residue: 0.0807 time to fit residues: 19.8520 Evaluate side-chains 192 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 45 THR 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 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 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 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 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 162 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 219 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 94 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.097537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.081501 restraints weight = 20052.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.083969 restraints weight = 10622.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.085604 restraints weight = 7063.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.086434 restraints weight = 5400.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.087216 restraints weight = 4637.360| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6465 Z= 0.115 Angle : 0.612 11.312 8817 Z= 0.308 Chirality : 0.041 0.133 1110 Planarity : 0.004 0.040 1095 Dihedral : 4.543 21.240 888 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 5.23 % Allowed : 23.83 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.29), residues: 834 helix: 0.15 (0.35), residues: 213 sheet: -0.39 (0.42), residues: 132 loop : 0.66 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 19 TYR 0.021 0.002 TYR A 103 PHE 0.013 0.001 PHE A 50 TRP 0.004 0.001 TRP C 80 HIS 0.003 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6465) covalent geometry : angle 0.61205 ( 8817) hydrogen bonds : bond 0.03369 ( 222) hydrogen bonds : angle 4.94665 ( 588) *********************** 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 197 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8245 (tp) REVERT: A 41 LYS cc_start: 0.9207 (ttmm) cc_final: 0.8754 (tttp) REVERT: A 182 TYR cc_start: 0.7486 (p90) cc_final: 0.6842 (p90) REVERT: A 243 SER cc_start: 0.8596 (m) cc_final: 0.8343 (t) REVERT: B 8 ARG cc_start: 0.8202 (ttt-90) cc_final: 0.7724 (ttt180) REVERT: B 19 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7522 (ptt-90) REVERT: B 73 ASP cc_start: 0.8495 (t70) cc_final: 0.7931 (t0) REVERT: B 76 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8217 (ptp-110) REVERT: B 196 MET cc_start: 0.7400 (mmp) cc_final: 0.7191 (mmp) REVERT: B 230 TYR cc_start: 0.7998 (t80) cc_final: 0.7736 (t80) REVERT: B 266 GLN cc_start: 0.8623 (mt0) cc_final: 0.8347 (mt0) REVERT: B 269 GLU cc_start: 0.9006 (mp0) cc_final: 0.8659 (mp0) REVERT: C 84 MET cc_start: 0.8773 (tpt) cc_final: 0.8491 (tpp) REVERT: C 90 MET cc_start: 0.8778 (mmm) cc_final: 0.8060 (mmp) REVERT: C 93 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8402 (p0) REVERT: C 98 ARG cc_start: 0.8732 (mtm110) cc_final: 0.8199 (mtm180) REVERT: C 125 LEU cc_start: 0.9043 (pp) cc_final: 0.8825 (pt) REVERT: C 148 TYR cc_start: 0.7518 (t80) cc_final: 0.6981 (t80) outliers start: 38 outliers final: 30 residues processed: 184 average time/residue: 0.0805 time to fit residues: 19.7900 Evaluate side-chains 186 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 45 THR 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 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 261 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 76 ARG 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 222 GLU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 105 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 195 ASN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 219 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 25 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.096084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.080085 restraints weight = 20065.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.082423 restraints weight = 10507.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.084023 restraints weight = 7068.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.085088 restraints weight = 5461.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.085509 restraints weight = 4570.760| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6465 Z= 0.168 Angle : 0.649 8.075 8817 Z= 0.331 Chirality : 0.042 0.171 1110 Planarity : 0.004 0.055 1095 Dihedral : 4.681 23.187 888 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 6.75 % Allowed : 22.87 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.29), residues: 834 helix: -0.00 (0.35), residues: 213 sheet: -0.73 (0.41), residues: 138 loop : 0.63 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 19 TYR 0.024 0.002 TYR B 148 PHE 0.016 0.002 PHE A 145 TRP 0.005 0.001 TRP C 80 HIS 0.004 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6465) covalent geometry : angle 0.64931 ( 8817) hydrogen bonds : bond 0.03525 ( 222) hydrogen bonds : angle 5.06122 ( 588) *********************** 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 206 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 157 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8204 (tp) REVERT: A 41 LYS cc_start: 0.9219 (ttmm) cc_final: 0.8810 (tttp) REVERT: A 182 TYR cc_start: 0.7522 (p90) cc_final: 0.6872 (p90) REVERT: A 243 SER cc_start: 0.8644 (m) cc_final: 0.8401 (t) REVERT: B 8 ARG cc_start: 0.8236 (ttt-90) cc_final: 0.7750 (ttt180) REVERT: B 19 ARG cc_start: 0.7939 (mtm-85) cc_final: 0.7493 (ptt-90) REVERT: B 73 ASP cc_start: 0.8536 (t70) cc_final: 0.7988 (t0) REVERT: B 76 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8262 (ptp-110) REVERT: B 87 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8279 (tm-30) REVERT: B 196 MET cc_start: 0.7555 (mmp) cc_final: 0.7350 (mmp) REVERT: B 230 TYR cc_start: 0.7931 (t80) cc_final: 0.7689 (t80) REVERT: B 266 GLN cc_start: 0.8617 (mt0) cc_final: 0.8350 (mt0) REVERT: B 269 GLU cc_start: 0.8970 (mp0) cc_final: 0.8667 (mp0) REVERT: C 84 MET cc_start: 0.8789 (tpt) cc_final: 0.8583 (tpp) REVERT: C 93 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8312 (p0) REVERT: C 98 ARG cc_start: 0.8705 (mtm110) cc_final: 0.8085 (mtm180) REVERT: C 125 LEU cc_start: 0.9079 (pp) cc_final: 0.8850 (pt) REVERT: C 148 TYR cc_start: 0.7539 (t80) cc_final: 0.7001 (t80) outliers start: 49 outliers final: 42 residues processed: 188 average time/residue: 0.0846 time to fit residues: 21.0288 Evaluate side-chains 198 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 68 HIS Chi-restraints excluded: chain A residue 87 GLN 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 A residue 272 VAL 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 76 ARG 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 222 GLU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 276 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 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 195 ASN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 251 THR 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 32 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 68 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.095992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.079938 restraints weight = 20253.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.082372 restraints weight = 10550.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.084013 restraints weight = 7019.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.085008 restraints weight = 5365.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.085739 restraints weight = 4528.872| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6465 Z= 0.163 Angle : 0.668 9.320 8817 Z= 0.334 Chirality : 0.042 0.159 1110 Planarity : 0.004 0.046 1095 Dihedral : 4.736 23.846 888 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 6.34 % Allowed : 23.28 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.28), residues: 834 helix: -0.07 (0.35), residues: 213 sheet: -0.53 (0.44), residues: 114 loop : 0.48 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 19 TYR 0.026 0.002 TYR B 148 PHE 0.037 0.002 PHE B 166 TRP 0.004 0.001 TRP C 80 HIS 0.004 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 6465) covalent geometry : angle 0.66768 ( 8817) hydrogen bonds : bond 0.03488 ( 222) hydrogen bonds : angle 5.09030 ( 588) *********************** 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 206 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8245 (tp) REVERT: A 41 LYS cc_start: 0.9236 (ttmm) cc_final: 0.8821 (tttp) REVERT: A 182 TYR cc_start: 0.7523 (p90) cc_final: 0.6900 (p90) REVERT: A 243 SER cc_start: 0.8635 (m) cc_final: 0.8399 (t) REVERT: B 8 ARG cc_start: 0.8244 (ttt-90) cc_final: 0.7746 (ttt180) REVERT: B 19 ARG cc_start: 0.7930 (mtm-85) cc_final: 0.7468 (ptt-90) REVERT: B 73 ASP cc_start: 0.8576 (t70) cc_final: 0.7986 (t0) REVERT: B 76 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8227 (ptp-110) REVERT: B 196 MET cc_start: 0.7596 (mmp) cc_final: 0.7380 (mmp) REVERT: B 223 ARG cc_start: 0.8182 (mtt180) cc_final: 0.7773 (mtt90) REVERT: B 230 TYR cc_start: 0.7978 (t80) cc_final: 0.7708 (t80) REVERT: B 266 GLN cc_start: 0.8657 (mt0) cc_final: 0.8378 (mt0) REVERT: B 269 GLU cc_start: 0.8967 (mp0) cc_final: 0.8485 (mp0) REVERT: C 84 MET cc_start: 0.8833 (tpt) cc_final: 0.8612 (tpp) REVERT: C 98 ARG cc_start: 0.8721 (mtm110) cc_final: 0.8069 (mtm180) REVERT: C 125 LEU cc_start: 0.9106 (pp) cc_final: 0.8890 (pt) REVERT: C 148 TYR cc_start: 0.7494 (t80) cc_final: 0.6889 (t80) outliers start: 46 outliers final: 42 residues processed: 191 average time/residue: 0.0806 time to fit residues: 20.4445 Evaluate side-chains 199 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 68 HIS 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 A residue 272 VAL 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 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 219 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 243 SER 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 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 195 ASN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 251 THR 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 21 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 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 = 0.3405 r_free = 0.3405 target = 0.092995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.076930 restraints weight = 20150.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.079313 restraints weight = 10505.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.080882 restraints weight = 6997.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.081848 restraints weight = 5361.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.082597 restraints weight = 4535.070| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 6465 Z= 0.293 Angle : 0.785 12.524 8817 Z= 0.399 Chirality : 0.045 0.194 1110 Planarity : 0.004 0.048 1095 Dihedral : 5.275 27.724 888 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.29), residues: 834 helix: -0.37 (0.35), residues: 207 sheet: -1.24 (0.39), residues: 150 loop : 0.51 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 19 TYR 0.027 0.003 TYR B 148 PHE 0.030 0.003 PHE C 166 TRP 0.005 0.001 TRP C 192 HIS 0.006 0.002 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00639 ( 6465) covalent geometry : angle 0.78496 ( 8817) hydrogen bonds : bond 0.04196 ( 222) hydrogen bonds : angle 5.56757 ( 588) ********************** 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 200 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8308 (tp) REVERT: A 41 LYS cc_start: 0.9255 (ttmm) cc_final: 0.8826 (tttp) REVERT: A 182 TYR cc_start: 0.7633 (p90) cc_final: 0.6936 (p90) REVERT: A 199 LEU cc_start: 0.8628 (mt) cc_final: 0.8394 (mt) REVERT: A 243 SER cc_start: 0.8663 (m) cc_final: 0.8448 (t) REVERT: A 261 SER cc_start: 0.9474 (OUTLIER) cc_final: 0.9258 (p) REVERT: B 8 ARG cc_start: 0.8317 (ttt-90) cc_final: 0.7802 (ttt180) REVERT: B 19 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7561 (ptt-90) REVERT: B 73 ASP cc_start: 0.8658 (t70) cc_final: 0.8220 (t0) REVERT: B 76 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8441 (ptp-110) REVERT: B 196 MET cc_start: 0.7631 (mmp) cc_final: 0.7425 (mmp) REVERT: B 266 GLN cc_start: 0.8644 (mt0) cc_final: 0.8388 (mt0) REVERT: B 269 GLU cc_start: 0.8990 (mp0) cc_final: 0.8587 (mp0) REVERT: C 98 ARG cc_start: 0.8713 (mtm110) cc_final: 0.8127 (mtm180) REVERT: C 125 LEU cc_start: 0.9207 (pp) cc_final: 0.8949 (pt) REVERT: C 148 TYR cc_start: 0.7506 (t80) cc_final: 0.6941 (t80) outliers start: 48 outliers final: 42 residues processed: 186 average time/residue: 0.0840 time to fit residues: 20.7445 Evaluate side-chains 194 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 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 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 15 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 VAL 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 219 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 276 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 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 195 ASN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 251 THR 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 28 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 69 optimal weight: 0.4980 chunk 14 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.095564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.079543 restraints weight = 20103.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.081965 restraints weight = 10575.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.083469 restraints weight = 7057.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.084554 restraints weight = 5466.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.085321 restraints weight = 4584.863| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6465 Z= 0.153 Angle : 0.724 13.561 8817 Z= 0.358 Chirality : 0.043 0.165 1110 Planarity : 0.004 0.047 1095 Dihedral : 4.968 24.854 888 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 6.34 % Allowed : 24.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.29), residues: 834 helix: -0.26 (0.35), residues: 207 sheet: -0.99 (0.42), residues: 120 loop : 0.46 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 19 TYR 0.025 0.002 TYR A 103 PHE 0.032 0.002 PHE B 166 TRP 0.004 0.001 TRP A 80 HIS 0.005 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6465) covalent geometry : angle 0.72418 ( 8817) hydrogen bonds : bond 0.03642 ( 222) hydrogen bonds : angle 5.29113 ( 588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1138.52 seconds wall clock time: 20 minutes 34.65 seconds (1234.65 seconds total)