Starting phenix.real_space_refine on Tue Feb 11 16:22:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k44_36872/02_2025/8k44_36872.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k44_36872/02_2025/8k44_36872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k44_36872/02_2025/8k44_36872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k44_36872/02_2025/8k44_36872.map" model { file = "/net/cci-nas-00/data/ceres_data/8k44_36872/02_2025/8k44_36872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k44_36872/02_2025/8k44_36872.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4053 2.51 5 N 1038 2.21 5 O 1236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6360 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2120 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 11, 'TRANS': 268} Chain: "B" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2120 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 11, 'TRANS': 268} Chain: "C" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2120 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 11, 'TRANS': 268} Time building chain proxies: 4.07, per 1000 atoms: 0.64 Number of scatterers: 6360 At special positions: 0 Unit cell: (91.2, 89.3, 97.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1236 8.00 N 1038 7.00 C 4053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 916.6 milliseconds 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 12 sheets defined 34.0% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 Processing helix chain 'A' and resid 23 through 28 removed outlier: 3.712A pdb=" N ALA A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 45 through 52 removed outlier: 3.625A pdb=" N GLU A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 69 removed outlier: 3.954A pdb=" N HIS A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 73 through 85 removed outlier: 4.233A pdb=" N ALA A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.964A pdb=" N ASN A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 215 " --> pdb=" O MET A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 219 through 223 removed outlier: 3.677A pdb=" N ARG A 223 " --> pdb=" O PRO A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 281 removed outlier: 4.203A pdb=" N ILE A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 16 removed outlier: 3.588A pdb=" N LEU B 13 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 28 removed outlier: 3.941A pdb=" N LEU B 26 " --> pdb=" O GLY B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 43 Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 62 through 69 removed outlier: 4.290A pdb=" N HIS B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 removed outlier: 4.108A pdb=" N ALA B 79 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 205 through 218 removed outlier: 3.597A pdb=" N ASN B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 270 through 281 removed outlier: 3.877A pdb=" N ASN B 274 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 281 " --> pdb=" O TYR B 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 16 removed outlier: 3.538A pdb=" N LYS C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 13 " --> pdb=" O ALA C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 27 Processing helix chain 'C' and resid 35 through 43 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.562A pdb=" N MET C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU C 53 " --> pdb=" O MET C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.896A pdb=" N HIS C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 72 Processing helix chain 'C' and resid 73 through 85 removed outlier: 3.823A pdb=" N PHE C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 205 through 218 removed outlier: 3.789A pdb=" N ASN C 213 " --> pdb=" O THR C 209 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 269 through 281 removed outlier: 4.246A pdb=" N ILE C 273 " --> pdb=" O GLU C 269 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN C 274 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR C 281 " --> pdb=" O TYR C 277 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 96 removed outlier: 7.151A pdb=" N LYS A 161 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 10.510A pdb=" N ASN A 151 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 11.004A pdb=" N THR A 159 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 181 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 239 " --> pdb=" O THR A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 105 Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 119 removed outlier: 6.356A pdb=" N THR A 115 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLY A 126 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 117 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 200 Processing sheet with id=AA5, first strand: chain 'B' and resid 95 through 96 Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AA7, first strand: chain 'B' and resid 115 through 119 removed outlier: 6.363A pdb=" N THR B 115 " --> pdb=" O GLY B 126 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY B 126 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B 117 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 197 through 200 Processing sheet with id=AA9, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.539A pdb=" N SER C 142 " --> pdb=" O THR C 264 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AB2, first strand: chain 'C' and resid 115 through 119 removed outlier: 6.466A pdb=" N THR C 115 " --> pdb=" O GLY C 126 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY C 126 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL C 117 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 128 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 198 through 200 222 hydrogen bonds defined for protein. 588 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2020 1.34 - 1.46: 1406 1.46 - 1.58: 2985 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 6465 Sorted by residual: bond pdb=" C THR B 237 " pdb=" N VAL B 238 " ideal model delta sigma weight residual 1.329 1.359 -0.030 1.32e-02 5.74e+03 5.24e+00 bond pdb=" C GLY B 228 " pdb=" N LEU B 229 " ideal model delta sigma weight residual 1.330 1.312 0.018 1.32e-02 5.74e+03 1.92e+00 bond pdb=" C LEU B 229 " pdb=" N TYR B 230 " ideal model delta sigma weight residual 1.331 1.313 0.019 1.38e-02 5.25e+03 1.81e+00 bond pdb=" C VAL B 238 " pdb=" N THR B 239 " ideal model delta sigma weight residual 1.330 1.349 -0.019 1.40e-02 5.10e+03 1.78e+00 bond pdb=" C ILE A 197 " pdb=" N LYS A 198 " ideal model delta sigma weight residual 1.330 1.341 -0.011 1.26e-02 6.30e+03 7.07e-01 ... (remaining 6460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 8734 1.88 - 3.76: 78 3.76 - 5.65: 2 5.65 - 7.53: 2 7.53 - 9.41: 1 Bond angle restraints: 8817 Sorted by residual: angle pdb=" C VAL B 227 " pdb=" N GLY B 228 " pdb=" CA GLY B 228 " ideal model delta sigma weight residual 122.33 120.11 2.22 7.30e-01 1.88e+00 9.28e+00 angle pdb=" CA LEU A 282 " pdb=" CB LEU A 282 " pdb=" CG LEU A 282 " ideal model delta sigma weight residual 116.30 125.71 -9.41 3.50e+00 8.16e-02 7.23e+00 angle pdb=" CA LEU B 125 " pdb=" CB LEU B 125 " pdb=" CG LEU B 125 " ideal model delta sigma weight residual 116.30 123.62 -7.32 3.50e+00 8.16e-02 4.38e+00 angle pdb=" N GLY B 228 " pdb=" CA GLY B 228 " pdb=" C GLY B 228 " ideal model delta sigma weight residual 111.04 114.60 -3.56 1.77e+00 3.19e-01 4.05e+00 angle pdb=" C MET B 196 " pdb=" N ILE B 197 " pdb=" CA ILE B 197 " ideal model delta sigma weight residual 122.91 120.35 2.56 1.43e+00 4.89e-01 3.21e+00 ... (remaining 8812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.69: 3650 14.69 - 29.39: 194 29.39 - 44.08: 39 44.08 - 58.77: 15 58.77 - 73.47: 2 Dihedral angle restraints: 3900 sinusoidal: 1449 harmonic: 2451 Sorted by residual: dihedral pdb=" CA TYR C 137 " pdb=" C TYR C 137 " pdb=" N SER C 138 " pdb=" CA SER C 138 " ideal model delta harmonic sigma weight residual 180.00 162.39 17.61 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA LEU A 279 " pdb=" C LEU A 279 " pdb=" N SER A 280 " pdb=" CA SER A 280 " ideal model delta harmonic sigma weight residual -180.00 -163.31 -16.69 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA SER B 138 " pdb=" C SER B 138 " pdb=" N ASN B 139 " pdb=" CA ASN B 139 " ideal model delta harmonic sigma weight residual -180.00 -164.02 -15.98 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 3897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 777 0.033 - 0.065: 215 0.065 - 0.098: 79 0.098 - 0.130: 36 0.130 - 0.163: 3 Chirality restraints: 1110 Sorted by residual: chirality pdb=" CG LEU A 282 " pdb=" CB LEU A 282 " pdb=" CD1 LEU A 282 " pdb=" CD2 LEU A 282 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CG LEU B 125 " pdb=" CB LEU B 125 " pdb=" CD1 LEU B 125 " pdb=" CD2 LEU B 125 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ILE A 252 " pdb=" N ILE A 252 " pdb=" C ILE A 252 " pdb=" CB ILE A 252 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1107 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 58 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO C 59 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 59 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 59 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 187 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO B 188 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 188 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 188 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 252 " 0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO C 253 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 253 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 253 " 0.014 5.00e-02 4.00e+02 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1165 2.76 - 3.30: 6745 3.30 - 3.83: 10484 3.83 - 4.37: 12270 4.37 - 4.90: 20879 Nonbonded interactions: 51543 Sorted by model distance: nonbonded pdb=" O GLY C 22 " pdb=" OG1 THR C 25 " model vdw 2.227 3.040 nonbonded pdb=" OG SER C 171 " pdb=" OG SER C 175 " model vdw 2.228 3.040 nonbonded pdb=" O PRO C 253 " pdb=" OG1 THR C 256 " model vdw 2.230 3.040 nonbonded pdb=" OG SER A 207 " pdb=" O LEU A 229 " model vdw 2.242 3.040 nonbonded pdb=" OG SER A 35 " pdb=" O SER C 30 " model vdw 2.250 3.040 ... (remaining 51538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 17.940 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.780 ------------------------------------------------------------------------------- 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= 0.231 Angle : 0.531 9.410 8817 Z= 0.303 Chirality : 0.039 0.163 1110 Planarity : 0.004 0.038 1095 Dihedral : 10.427 73.466 2316 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.41 % Allowed : 10.19 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.28), residues: 834 helix: 0.07 (0.37), residues: 201 sheet: 0.23 (0.43), residues: 114 loop : 0.78 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 192 HIS 0.002 0.001 HIS C 127 PHE 0.013 0.001 PHE A 50 TYR 0.006 0.001 TYR B 148 ARG 0.004 0.000 ARG C 223 *********************** 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 : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9140 (ttmm) cc_final: 0.8839 (tttt) REVERT: A 84 MET cc_start: 0.8695 (tpt) cc_final: 0.8417 (tpt) REVERT: A 99 MET cc_start: 0.8190 (mmm) cc_final: 0.7716 (mmm) REVERT: A 101 MET cc_start: 0.8431 (mtp) cc_final: 0.7599 (mtp) REVERT: A 167 ILE cc_start: 0.9317 (pt) cc_final: 0.9085 (pt) REVERT: A 182 TYR cc_start: 0.7773 (p90) cc_final: 0.6865 (p90) REVERT: A 243 SER cc_start: 0.8655 (m) cc_final: 0.8449 (t) REVERT: B 8 ARG cc_start: 0.8582 (ttt-90) cc_final: 0.7786 (ttt180) REVERT: B 73 ASP cc_start: 0.8843 (t70) cc_final: 0.8328 (t0) REVERT: B 84 MET cc_start: 0.8752 (tpt) cc_final: 0.8357 (tpp) REVERT: B 232 ASP cc_start: 0.6519 (t0) cc_final: 0.6136 (t0) REVERT: B 269 GLU cc_start: 0.9031 (mp0) cc_final: 0.8821 (mp0) REVERT: C 33 LYS cc_start: 0.8206 (mttp) cc_final: 0.7974 (mmtp) REVERT: C 84 MET cc_start: 0.8550 (tpt) cc_final: 0.8266 (tpp) REVERT: C 98 ARG cc_start: 0.8578 (mtm110) cc_final: 0.7793 (mtm180) REVERT: C 148 TYR cc_start: 0.7659 (t80) cc_final: 0.7222 (t80) REVERT: C 150 TYR cc_start: 0.7908 (t80) cc_final: 0.7697 (t80) outliers start: 3 outliers final: 1 residues processed: 218 average time/residue: 0.2164 time to fit residues: 59.8026 Evaluate side-chains 144 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 0.0040 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 HIS A 94 ASN ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN A 195 ASN A 216 ASN B 68 HIS B 102 GLN B 111 ASN C 94 ASN C 151 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.098566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.082481 restraints weight = 19617.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.084967 restraints weight = 10481.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.086567 restraints weight = 6984.992| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6465 Z= 0.176 Angle : 0.594 9.056 8817 Z= 0.311 Chirality : 0.042 0.161 1110 Planarity : 0.004 0.040 1095 Dihedral : 4.608 35.483 889 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.13 % Allowed : 16.53 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.28), residues: 834 helix: 0.21 (0.34), residues: 207 sheet: -0.09 (0.40), residues: 126 loop : 0.86 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 80 HIS 0.011 0.003 HIS B 68 PHE 0.013 0.002 PHE A 50 TYR 0.020 0.002 TYR B 148 ARG 0.007 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8421 (t70) cc_final: 0.8050 (t0) REVERT: A 84 MET cc_start: 0.8787 (tpt) cc_final: 0.8570 (tpt) REVERT: A 150 TYR cc_start: 0.7208 (t80) cc_final: 0.6869 (t80) REVERT: A 182 TYR cc_start: 0.7658 (p90) cc_final: 0.6819 (p90) REVERT: A 243 SER cc_start: 0.8614 (m) cc_final: 0.8340 (t) REVERT: B 8 ARG cc_start: 0.8507 (ttt-90) cc_final: 0.7877 (ttt180) REVERT: B 19 ARG cc_start: 0.7919 (mtm-85) cc_final: 0.7346 (ptt-90) REVERT: B 41 LYS cc_start: 0.9094 (ttmt) cc_final: 0.8675 (tttt) REVERT: B 73 ASP cc_start: 0.8496 (t70) cc_final: 0.7970 (t0) REVERT: B 84 MET cc_start: 0.8877 (tpt) cc_final: 0.8530 (tpp) REVERT: B 98 ARG cc_start: 0.8558 (mtm180) cc_final: 0.8265 (mtm180) REVERT: B 167 ILE cc_start: 0.9265 (pt) cc_final: 0.8910 (pt) REVERT: C 84 MET cc_start: 0.8917 (tpt) cc_final: 0.8673 (tpp) REVERT: C 98 ARG cc_start: 0.8650 (mtm110) cc_final: 0.8319 (mtm110) REVERT: C 148 TYR cc_start: 0.7722 (t80) cc_final: 0.7179 (t80) outliers start: 30 outliers final: 21 residues processed: 187 average time/residue: 0.1933 time to fit residues: 46.8512 Evaluate side-chains 174 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 76 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 HIS A 87 GLN A 94 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 HIS B 87 GLN ** 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 = 0.3467 r_free = 0.3467 target = 0.097197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.081516 restraints weight = 19595.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.083899 restraints weight = 10229.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085548 restraints weight = 6729.964| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6465 Z= 0.191 Angle : 0.583 7.066 8817 Z= 0.301 Chirality : 0.041 0.155 1110 Planarity : 0.004 0.043 1095 Dihedral : 4.531 27.894 889 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 5.10 % Allowed : 18.04 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.28), residues: 834 helix: 0.39 (0.35), residues: 207 sheet: -0.43 (0.39), residues: 138 loop : 0.81 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 80 HIS 0.006 0.002 HIS A 68 PHE 0.022 0.002 PHE A 166 TYR 0.018 0.002 TYR C 103 ARG 0.009 0.001 ARG C 19 *********************** 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 196 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 0.698 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: 0.7939 (mtm110) cc_final: 0.7614 (ptt-90) REVERT: A 49 MET cc_start: 0.8772 (mmp) cc_final: 0.8467 (mmp) REVERT: A 73 ASP cc_start: 0.8209 (t70) cc_final: 0.7974 (t0) REVERT: A 84 MET cc_start: 0.8843 (tpt) cc_final: 0.8621 (tpt) REVERT: A 166 PHE cc_start: 0.9219 (t80) cc_final: 0.8874 (t80) REVERT: A 182 TYR cc_start: 0.7671 (p90) cc_final: 0.6846 (p90) REVERT: A 243 SER cc_start: 0.8613 (m) cc_final: 0.8346 (t) REVERT: B 8 ARG cc_start: 0.8452 (ttt-90) cc_final: 0.7826 (ttt180) REVERT: B 19 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7371 (ptt-90) REVERT: B 41 LYS cc_start: 0.9135 (ttmt) cc_final: 0.8921 (tppt) REVERT: B 73 ASP cc_start: 0.8550 (t70) cc_final: 0.7880 (t0) REVERT: B 84 MET cc_start: 0.8882 (tpt) cc_final: 0.8541 (tpp) REVERT: B 230 TYR cc_start: 0.8061 (t80) cc_final: 0.7698 (t80) REVERT: C 84 MET cc_start: 0.8915 (tpt) cc_final: 0.8663 (tpp) REVERT: C 98 ARG cc_start: 0.8634 (mtm110) cc_final: 0.8067 (mtm180) REVERT: C 148 TYR cc_start: 0.7760 (t80) cc_final: 0.7196 (t80) outliers start: 37 outliers final: 29 residues processed: 180 average time/residue: 0.1890 time to fit residues: 44.3655 Evaluate side-chains 177 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 89 LEU 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 258 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 219 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 25 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 23 optimal weight: 0.0370 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 GLN A 94 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 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 = 0.3476 r_free = 0.3476 target = 0.097766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.081322 restraints weight = 19985.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.083787 restraints weight = 10658.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.085459 restraints weight = 7109.628| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6465 Z= 0.204 Angle : 0.574 6.832 8817 Z= 0.298 Chirality : 0.041 0.135 1110 Planarity : 0.004 0.042 1095 Dihedral : 4.473 19.565 888 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 5.79 % Allowed : 20.25 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.28), residues: 834 helix: 0.29 (0.35), residues: 207 sheet: -0.47 (0.39), residues: 138 loop : 0.78 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 80 HIS 0.008 0.002 HIS B 68 PHE 0.028 0.002 PHE B 166 TYR 0.021 0.002 TYR A 103 ARG 0.010 0.001 ARG C 19 *********************** 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 202 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8033 (mtm110) cc_final: 0.7722 (ptt-90) REVERT: A 84 MET cc_start: 0.8822 (tpt) cc_final: 0.8614 (tpt) REVERT: A 166 PHE cc_start: 0.9122 (t80) cc_final: 0.8734 (t80) REVERT: A 182 TYR cc_start: 0.7624 (p90) cc_final: 0.6863 (p90) REVERT: A 211 MET cc_start: 0.8615 (mpp) cc_final: 0.8395 (mpp) REVERT: A 243 SER cc_start: 0.8611 (m) cc_final: 0.8363 (t) REVERT: B 8 ARG cc_start: 0.8346 (ttt-90) cc_final: 0.7822 (ttt180) REVERT: B 19 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7238 (ptt-90) REVERT: B 73 ASP cc_start: 0.8393 (t70) cc_final: 0.7894 (t0) REVERT: B 84 MET cc_start: 0.8822 (tpt) cc_final: 0.8482 (tpp) REVERT: B 90 MET cc_start: 0.8350 (mmp) cc_final: 0.8136 (mmp) REVERT: B 196 MET cc_start: 0.7294 (mmp) cc_final: 0.7042 (mmp) REVERT: B 230 TYR cc_start: 0.8101 (t80) cc_final: 0.7725 (t80) REVERT: B 269 GLU cc_start: 0.8993 (mp0) cc_final: 0.8737 (mp0) REVERT: C 84 MET cc_start: 0.8846 (tpt) cc_final: 0.8575 (tpp) REVERT: C 98 ARG cc_start: 0.8659 (mtm110) cc_final: 0.8274 (mtm180) REVERT: C 148 TYR cc_start: 0.7698 (t80) cc_final: 0.7098 (t80) REVERT: C 236 VAL cc_start: 0.8038 (OUTLIER) cc_final: 0.7678 (t) outliers start: 42 outliers final: 31 residues processed: 184 average time/residue: 0.1800 time to fit residues: 43.4753 Evaluate side-chains 184 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 91 ILE Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 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 68 HIS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 236 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.093358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.077259 restraints weight = 20249.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.079579 restraints weight = 10740.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.081136 restraints weight = 7201.023| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 6465 Z= 0.411 Angle : 0.686 7.256 8817 Z= 0.366 Chirality : 0.044 0.152 1110 Planarity : 0.004 0.045 1095 Dihedral : 5.208 25.849 888 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 8.68 % Allowed : 17.91 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.28), residues: 834 helix: -0.32 (0.34), residues: 207 sheet: -0.73 (0.43), residues: 120 loop : 0.51 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 80 HIS 0.005 0.002 HIS B 127 PHE 0.023 0.003 PHE A 166 TYR 0.023 0.002 TYR A 103 ARG 0.011 0.001 ARG C 19 *********************** 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 214 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 151 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8130 (mtm110) cc_final: 0.7748 (ptt-90) REVERT: A 87 GLN cc_start: 0.8632 (tp-100) cc_final: 0.8193 (tm-30) REVERT: A 182 TYR cc_start: 0.7621 (p90) cc_final: 0.6820 (p90) REVERT: A 211 MET cc_start: 0.8757 (mpp) cc_final: 0.8488 (mpp) REVERT: A 243 SER cc_start: 0.8710 (m) cc_final: 0.8473 (t) REVERT: B 8 ARG cc_start: 0.8401 (ttt-90) cc_final: 0.7836 (ttt180) REVERT: B 19 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7284 (ptt-90) REVERT: B 73 ASP cc_start: 0.8596 (t70) cc_final: 0.8235 (t0) REVERT: B 76 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8491 (ptp-110) REVERT: B 223 ARG cc_start: 0.8057 (mtt90) cc_final: 0.7739 (mtt90) REVERT: B 269 GLU cc_start: 0.9002 (mp0) cc_final: 0.8681 (mp0) REVERT: C 98 ARG cc_start: 0.8672 (mtm110) cc_final: 0.8319 (mtm180) REVERT: C 148 TYR cc_start: 0.7773 (t80) cc_final: 0.7243 (t80) REVERT: C 236 VAL cc_start: 0.8080 (OUTLIER) cc_final: 0.7878 (t) outliers start: 63 outliers final: 44 residues processed: 197 average time/residue: 0.1841 time to fit residues: 47.6472 Evaluate side-chains 186 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 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 61 ILE Chi-restraints excluded: chain B residue 68 HIS 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 168 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 252 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 50 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 21 optimal weight: 0.3980 chunk 68 optimal weight: 0.0070 chunk 71 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 52 optimal weight: 0.0970 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 ASN A 191 ASN A 216 ASN C 93 ASN C 94 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.097538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.081563 restraints weight = 19859.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.083950 restraints weight = 10197.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.085638 restraints weight = 6710.996| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6465 Z= 0.163 Angle : 0.605 9.058 8817 Z= 0.305 Chirality : 0.041 0.132 1110 Planarity : 0.003 0.039 1095 Dihedral : 4.538 21.392 888 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.13 % Allowed : 23.97 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.28), residues: 834 helix: 0.03 (0.35), residues: 207 sheet: -0.25 (0.43), residues: 120 loop : 0.47 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 80 HIS 0.003 0.001 HIS B 127 PHE 0.032 0.002 PHE B 166 TYR 0.023 0.002 TYR A 103 ARG 0.012 0.001 ARG C 19 *********************** 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 196 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8240 (tp) REVERT: A 19 ARG cc_start: 0.7990 (mtm110) cc_final: 0.7703 (ptt-90) REVERT: A 52 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8011 (mm-30) REVERT: A 182 TYR cc_start: 0.7621 (p90) cc_final: 0.6902 (p90) REVERT: A 211 MET cc_start: 0.8809 (mpp) cc_final: 0.8453 (mpp) REVERT: A 243 SER cc_start: 0.8623 (m) cc_final: 0.8361 (t) REVERT: B 8 ARG cc_start: 0.8229 (ttt-90) cc_final: 0.7731 (ttt180) REVERT: B 19 ARG cc_start: 0.7891 (mtm-85) cc_final: 0.7329 (ptt-90) REVERT: B 53 LEU cc_start: 0.9356 (mt) cc_final: 0.9065 (mt) REVERT: B 73 ASP cc_start: 0.8450 (t70) cc_final: 0.7696 (t0) REVERT: B 230 TYR cc_start: 0.8103 (t80) cc_final: 0.7840 (t80) REVERT: C 125 LEU cc_start: 0.9083 (pp) cc_final: 0.8841 (pt) REVERT: C 148 TYR cc_start: 0.7503 (t80) cc_final: 0.6959 (t80) REVERT: C 236 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7804 (t) outliers start: 30 outliers final: 23 residues processed: 184 average time/residue: 0.1724 time to fit residues: 41.8389 Evaluate side-chains 173 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 94 ASN Chi-restraints excluded: chain A residue 137 TYR 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 229 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 236 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 23 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 68 optimal weight: 0.5980 chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN C 94 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.095178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.079074 restraints weight = 20027.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.081396 restraints weight = 10476.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.082967 restraints weight = 7037.679| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6465 Z= 0.311 Angle : 0.692 10.095 8817 Z= 0.350 Chirality : 0.043 0.208 1110 Planarity : 0.004 0.041 1095 Dihedral : 4.896 23.503 888 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 6.34 % Allowed : 23.69 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.28), residues: 834 helix: -0.32 (0.35), residues: 207 sheet: -0.75 (0.43), residues: 120 loop : 0.46 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 80 HIS 0.004 0.002 HIS B 127 PHE 0.025 0.003 PHE C 166 TYR 0.026 0.003 TYR C 150 ARG 0.006 0.001 ARG C 19 *********************** 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 201 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8272 (tp) REVERT: A 19 ARG cc_start: 0.8117 (mtm110) cc_final: 0.7900 (ptt-90) REVERT: A 182 TYR cc_start: 0.7575 (p90) cc_final: 0.6877 (p90) REVERT: A 211 MET cc_start: 0.8859 (mpp) cc_final: 0.8501 (mpp) REVERT: A 243 SER cc_start: 0.8672 (m) cc_final: 0.8430 (t) REVERT: B 8 ARG cc_start: 0.8297 (ttt-90) cc_final: 0.7745 (ttt180) REVERT: B 19 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7511 (ptt-90) REVERT: B 73 ASP cc_start: 0.8622 (t70) cc_final: 0.8127 (t0) REVERT: B 87 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8290 (tm-30) REVERT: B 196 MET cc_start: 0.7412 (tpp) cc_final: 0.7144 (tpt) REVERT: B 230 TYR cc_start: 0.8105 (t80) cc_final: 0.7831 (t80) REVERT: C 125 LEU cc_start: 0.9161 (pp) cc_final: 0.8899 (pt) REVERT: C 148 TYR cc_start: 0.7557 (t80) cc_final: 0.7013 (t80) REVERT: C 236 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7891 (t) outliers start: 46 outliers final: 39 residues processed: 184 average time/residue: 0.1648 time to fit residues: 40.7277 Evaluate side-chains 188 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain 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 68 HIS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 259 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 13 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 ** 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 = 0.3451 r_free = 0.3451 target = 0.095915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.079841 restraints weight = 19798.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.082207 restraints weight = 10335.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.083801 restraints weight = 6888.346| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3615 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= 0.242 Angle : 0.675 11.946 8817 Z= 0.337 Chirality : 0.042 0.197 1110 Planarity : 0.004 0.041 1095 Dihedral : 4.782 22.543 888 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 6.34 % Allowed : 24.38 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.28), residues: 834 helix: -0.32 (0.35), residues: 207 sheet: -0.80 (0.43), residues: 120 loop : 0.47 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 80 HIS 0.004 0.001 HIS B 127 PHE 0.026 0.002 PHE C 166 TYR 0.026 0.002 TYR A 103 ARG 0.009 0.001 ARG C 19 *********************** 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 204 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8290 (tp) REVERT: A 19 ARG cc_start: 0.8066 (mtm110) cc_final: 0.7803 (ptt-90) REVERT: A 87 GLN cc_start: 0.8624 (tp-100) cc_final: 0.8414 (tm-30) REVERT: A 182 TYR cc_start: 0.7483 (p90) cc_final: 0.6833 (p90) REVERT: A 211 MET cc_start: 0.8830 (mpp) cc_final: 0.8478 (mpp) REVERT: A 243 SER cc_start: 0.8684 (m) cc_final: 0.8428 (t) REVERT: B 8 ARG cc_start: 0.8277 (ttt-90) cc_final: 0.7746 (ttt180) REVERT: B 19 ARG cc_start: 0.7981 (mtm-85) cc_final: 0.7525 (ptt-90) REVERT: B 73 ASP cc_start: 0.8567 (t70) cc_final: 0.8071 (t0) REVERT: B 87 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8317 (tm-30) REVERT: B 182 TYR cc_start: 0.7937 (p90) cc_final: 0.7317 (p90) REVERT: B 223 ARG cc_start: 0.8051 (mtt90) cc_final: 0.7317 (mpt180) REVERT: B 230 TYR cc_start: 0.8123 (t80) cc_final: 0.7796 (t80) REVERT: C 125 LEU cc_start: 0.9154 (pp) cc_final: 0.8924 (pt) REVERT: C 148 TYR cc_start: 0.7519 (t80) cc_final: 0.6995 (t80) REVERT: C 236 VAL cc_start: 0.8101 (OUTLIER) cc_final: 0.7840 (t) outliers start: 46 outliers final: 39 residues processed: 186 average time/residue: 0.1785 time to fit residues: 44.0369 Evaluate side-chains 187 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain 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 68 HIS 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 243 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 259 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 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 = 0.3461 r_free = 0.3461 target = 0.096372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.080384 restraints weight = 19961.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.082801 restraints weight = 10380.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.084360 restraints weight = 6907.866| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3727 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= 0.219 Angle : 0.690 13.108 8817 Z= 0.342 Chirality : 0.043 0.243 1110 Planarity : 0.004 0.040 1095 Dihedral : 4.653 17.136 888 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 5.51 % Allowed : 25.34 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.28), residues: 834 helix: -0.45 (0.34), residues: 213 sheet: -0.63 (0.42), residues: 114 loop : 0.47 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 80 HIS 0.004 0.001 HIS B 127 PHE 0.029 0.002 PHE C 166 TYR 0.026 0.002 TYR B 148 ARG 0.008 0.001 ARG C 19 *********************** 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 198 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8268 (tp) REVERT: A 182 TYR cc_start: 0.7456 (p90) cc_final: 0.6819 (p90) REVERT: A 211 MET cc_start: 0.8867 (mpp) cc_final: 0.8514 (mpp) REVERT: A 243 SER cc_start: 0.8698 (m) cc_final: 0.8426 (t) REVERT: B 8 ARG cc_start: 0.8254 (ttt-90) cc_final: 0.7730 (ttt180) REVERT: B 19 ARG cc_start: 0.8022 (mtm-85) cc_final: 0.7552 (ptt-90) REVERT: B 73 ASP cc_start: 0.8564 (t70) cc_final: 0.8005 (t0) REVERT: B 87 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8320 (tm-30) REVERT: B 196 MET cc_start: 0.7669 (tpt) cc_final: 0.7425 (tpt) REVERT: B 223 ARG cc_start: 0.8000 (mtt90) cc_final: 0.7318 (mpt180) REVERT: B 230 TYR cc_start: 0.8176 (t80) cc_final: 0.7858 (t80) REVERT: C 98 ARG cc_start: 0.8830 (mtm110) cc_final: 0.8185 (mtm180) REVERT: C 125 LEU cc_start: 0.9146 (pp) cc_final: 0.8940 (pt) REVERT: C 148 TYR cc_start: 0.7553 (t80) cc_final: 0.7020 (t80) REVERT: C 236 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7714 (t) outliers start: 40 outliers final: 35 residues processed: 186 average time/residue: 0.1758 time to fit residues: 43.2706 Evaluate side-chains 186 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 55 GLN Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 279 LEU 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 91 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 259 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 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 = 0.3436 r_free = 0.3436 target = 0.094812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.078843 restraints weight = 20087.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.081178 restraints weight = 10579.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.082787 restraints weight = 7052.305| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6465 Z= 0.307 Angle : 0.739 11.833 8817 Z= 0.371 Chirality : 0.044 0.241 1110 Planarity : 0.004 0.048 1095 Dihedral : 4.943 18.660 888 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.92 % Allowed : 25.07 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.28), residues: 834 helix: -0.47 (0.35), residues: 207 sheet: -0.74 (0.43), residues: 114 loop : 0.41 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 80 HIS 0.005 0.002 HIS B 127 PHE 0.031 0.003 PHE C 166 TYR 0.030 0.003 TYR B 148 ARG 0.011 0.001 ARG C 19 ********************** 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 197 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8296 (tp) REVERT: A 87 GLN cc_start: 0.8500 (tm-30) cc_final: 0.8111 (tm-30) REVERT: A 182 TYR cc_start: 0.7476 (p90) cc_final: 0.6846 (p90) REVERT: A 211 MET cc_start: 0.8834 (mpp) cc_final: 0.8487 (mpp) REVERT: A 243 SER cc_start: 0.8696 (m) cc_final: 0.8440 (t) REVERT: B 8 ARG cc_start: 0.8296 (ttt-90) cc_final: 0.7754 (ttt180) REVERT: B 19 ARG cc_start: 0.7980 (mtm-85) cc_final: 0.7478 (ptt-90) REVERT: B 73 ASP cc_start: 0.8668 (t70) cc_final: 0.8168 (t0) REVERT: B 87 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8327 (tm-30) REVERT: B 230 TYR cc_start: 0.8148 (t80) cc_final: 0.7785 (t80) REVERT: C 98 ARG cc_start: 0.8806 (mtm110) cc_final: 0.8143 (mtm180) REVERT: C 125 LEU cc_start: 0.9172 (pp) cc_final: 0.8954 (pt) REVERT: C 148 TYR cc_start: 0.7572 (t80) cc_final: 0.7025 (t80) REVERT: C 236 VAL cc_start: 0.8084 (OUTLIER) cc_final: 0.7806 (t) outliers start: 43 outliers final: 38 residues processed: 183 average time/residue: 0.2118 time to fit residues: 51.4489 Evaluate side-chains 190 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 279 LEU 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 91 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 259 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 22 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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** B 68 HIS ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.097008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.080954 restraints weight = 20276.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.083390 restraints weight = 10428.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.084999 restraints weight = 6900.534| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6465 Z= 0.203 Angle : 0.727 13.557 8817 Z= 0.354 Chirality : 0.043 0.254 1110 Planarity : 0.004 0.039 1095 Dihedral : 4.696 18.280 888 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 5.10 % Allowed : 26.03 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.29), residues: 834 helix: -0.29 (0.35), residues: 207 sheet: -0.80 (0.43), residues: 120 loop : 0.49 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 80 HIS 0.004 0.001 HIS B 127 PHE 0.031 0.002 PHE C 166 TYR 0.025 0.002 TYR A 103 ARG 0.012 0.001 ARG C 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2069.71 seconds wall clock time: 38 minutes 14.63 seconds (2294.63 seconds total)