Starting phenix.real_space_refine on Fri Jul 19 03:26:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k44_36872/07_2024/8k44_36872.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k44_36872/07_2024/8k44_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k44_36872/07_2024/8k44_36872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k44_36872/07_2024/8k44_36872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k44_36872/07_2024/8k44_36872.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k44_36872/07_2024/8k44_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 Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 73": "OD1" <-> "OD2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 149": "OE1" <-> "OE2" Residue "C TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 3.93, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 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: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.81 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: 1.59 Time building geometry restraints manager: 2.82 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: 99.98 - 106.79: 166 106.79 - 113.59: 3868 113.59 - 120.40: 2151 120.40 - 127.20: 2588 127.20 - 134.01: 44 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 2.440 nonbonded pdb=" OG SER C 171 " pdb=" OG SER C 175 " model vdw 2.228 2.440 nonbonded pdb=" O PRO C 253 " pdb=" OG1 THR C 256 " model vdw 2.230 2.440 nonbonded pdb=" OG SER A 207 " pdb=" O LEU A 229 " model vdw 2.242 2.440 nonbonded pdb=" OG SER A 35 " pdb=" O SER C 30 " model vdw 2.250 2.440 ... (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 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: 0.250 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.140 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.510 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 216 time to evaluate : 0.798 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: 0.2050 time to fit residues: 56.6582 Evaluate side-chains 144 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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: 0.7980 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 42 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 135 ASN A 139 ASN A 155 ASN A 191 ASN A 195 ASN A 216 ASN B 68 HIS B 102 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN C 178 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2259 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= 0.210 Angle : 0.584 8.860 8817 Z= 0.308 Chirality : 0.041 0.155 1110 Planarity : 0.004 0.043 1095 Dihedral : 4.761 36.443 889 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.65 % Allowed : 16.39 % Favored : 77.96 % 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: 0.58 (0.28), residues: 834 helix: 0.18 (0.35), residues: 207 sheet: -0.20 (0.40), residues: 126 loop : 0.84 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 80 HIS 0.011 0.003 HIS B 68 PHE 0.013 0.002 PHE A 50 TYR 0.021 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 206 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 165 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8724 (ttt180) cc_final: 0.8520 (ptm160) REVERT: A 41 LYS cc_start: 0.9218 (ttmm) cc_final: 0.8810 (tttt) REVERT: A 73 ASP cc_start: 0.8447 (t70) cc_final: 0.8127 (t0) REVERT: A 84 MET cc_start: 0.8784 (tpt) cc_final: 0.8572 (tpt) REVERT: A 150 TYR cc_start: 0.7251 (t80) cc_final: 0.7029 (t80) REVERT: A 182 TYR cc_start: 0.7563 (p90) cc_final: 0.6765 (p90) REVERT: A 243 SER cc_start: 0.8699 (m) cc_final: 0.8458 (t) REVERT: B 8 ARG cc_start: 0.8481 (ttt-90) cc_final: 0.7892 (ttt180) REVERT: B 19 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.6828 (ptt90) REVERT: B 38 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7389 (mt-10) REVERT: B 73 ASP cc_start: 0.8521 (t70) cc_final: 0.8002 (t0) REVERT: B 84 MET cc_start: 0.8874 (tpt) cc_final: 0.8514 (tpp) REVERT: B 98 ARG cc_start: 0.8602 (mtm180) cc_final: 0.8284 (mtm180) REVERT: B 167 ILE cc_start: 0.9327 (pt) cc_final: 0.8971 (pt) REVERT: C 33 LYS cc_start: 0.8131 (mttp) cc_final: 0.7888 (mmtp) REVERT: C 84 MET cc_start: 0.8946 (tpt) cc_final: 0.8713 (tpp) REVERT: C 97 VAL cc_start: 0.9080 (m) cc_final: 0.8713 (p) REVERT: C 98 ARG cc_start: 0.8577 (mtm110) cc_final: 0.7849 (mtm180) REVERT: C 148 TYR cc_start: 0.7682 (t80) cc_final: 0.7136 (t80) REVERT: C 211 MET cc_start: 0.9075 (mtp) cc_final: 0.8744 (mtm) outliers start: 41 outliers final: 30 residues processed: 192 average time/residue: 0.1886 time to fit residues: 46.9568 Evaluate side-chains 180 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 150 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 32 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 VAL 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 110 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain 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 89 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 251 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 21 optimal weight: 0.1980 chunk 76 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 A 274 ASN B 68 HIS B 87 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6465 Z= 0.149 Angle : 0.567 9.867 8817 Z= 0.288 Chirality : 0.040 0.141 1110 Planarity : 0.004 0.041 1095 Dihedral : 4.399 29.301 889 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 5.10 % Allowed : 19.01 % Favored : 75.90 % 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: 0.59 (0.28), residues: 834 helix: 0.43 (0.35), residues: 207 sheet: -0.55 (0.38), residues: 138 loop : 0.87 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 80 HIS 0.013 0.003 HIS B 68 PHE 0.021 0.002 PHE B 166 TYR 0.019 0.002 TYR C 103 ARG 0.008 0.000 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 204 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 167 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8726 (ttt180) cc_final: 0.8526 (ptm160) REVERT: A 19 ARG cc_start: 0.7778 (mtm110) cc_final: 0.7366 (ptt-90) REVERT: A 41 LYS cc_start: 0.9186 (ttmm) cc_final: 0.8827 (tttp) REVERT: A 73 ASP cc_start: 0.8149 (t70) cc_final: 0.7946 (t0) REVERT: A 98 ARG cc_start: 0.8490 (mtm180) cc_final: 0.8051 (mtm180) REVERT: A 150 TYR cc_start: 0.7165 (t80) cc_final: 0.6963 (t80) REVERT: A 166 PHE cc_start: 0.9219 (t80) cc_final: 0.8789 (t80) REVERT: A 182 TYR cc_start: 0.7635 (p90) cc_final: 0.6881 (p90) REVERT: A 243 SER cc_start: 0.8712 (m) cc_final: 0.8465 (t) REVERT: B 8 ARG cc_start: 0.8357 (ttt-90) cc_final: 0.7820 (ttt180) REVERT: B 19 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.6867 (ptt90) REVERT: B 38 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7497 (mt-10) REVERT: B 41 LYS cc_start: 0.9125 (ttmt) cc_final: 0.8923 (tppt) REVERT: B 73 ASP cc_start: 0.8429 (t70) cc_final: 0.7817 (t0) REVERT: B 84 MET cc_start: 0.8791 (tpt) cc_final: 0.8405 (tpp) REVERT: B 230 TYR cc_start: 0.7807 (t80) cc_final: 0.7272 (t80) REVERT: B 232 ASP cc_start: 0.6700 (t0) cc_final: 0.6495 (t0) REVERT: C 84 MET cc_start: 0.8843 (tpt) cc_final: 0.8586 (tpp) REVERT: C 98 ARG cc_start: 0.8538 (mtm110) cc_final: 0.8133 (mtm180) REVERT: C 148 TYR cc_start: 0.7662 (t80) cc_final: 0.7083 (t80) outliers start: 37 outliers final: 23 residues processed: 186 average time/residue: 0.1871 time to fit residues: 45.3663 Evaluate side-chains 170 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 32 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 110 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 229 LEU Chi-restraints excluded: chain B residue 34 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 C residue 40 GLU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 251 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 21 optimal weight: 0.3980 overall best weight: 5.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 6465 Z= 0.378 Angle : 0.651 6.945 8817 Z= 0.344 Chirality : 0.042 0.130 1110 Planarity : 0.004 0.045 1095 Dihedral : 4.986 21.421 889 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 7.99 % Allowed : 19.15 % Favored : 72.87 % 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: 0.36 (0.29), residues: 834 helix: 0.08 (0.35), residues: 210 sheet: -0.46 (0.41), residues: 126 loop : 0.69 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 80 HIS 0.010 0.003 HIS B 68 PHE 0.025 0.003 PHE B 166 TYR 0.024 0.002 TYR C 150 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 206 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 148 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8276 (tp) REVERT: A 19 ARG cc_start: 0.8003 (mtm110) cc_final: 0.7514 (ptt-90) REVERT: A 41 LYS cc_start: 0.9221 (ttmm) cc_final: 0.8855 (tttt) REVERT: A 98 ARG cc_start: 0.8504 (mtm180) cc_final: 0.8275 (mtm180) REVERT: A 166 PHE cc_start: 0.9200 (t80) cc_final: 0.8934 (t80) REVERT: A 182 TYR cc_start: 0.7623 (p90) cc_final: 0.6809 (p90) REVERT: A 243 SER cc_start: 0.8723 (m) cc_final: 0.8494 (t) REVERT: B 8 ARG cc_start: 0.8434 (ttt-90) cc_final: 0.7857 (ttt180) REVERT: B 19 ARG cc_start: 0.7718 (mtm-85) cc_final: 0.7057 (ptt-90) REVERT: B 40 GLU cc_start: 0.8295 (pt0) cc_final: 0.8077 (pt0) REVERT: B 55 GLN cc_start: 0.8981 (pm20) cc_final: 0.8661 (pm20) REVERT: B 73 ASP cc_start: 0.8594 (t70) cc_final: 0.8118 (t0) REVERT: C 84 MET cc_start: 0.8921 (tpt) cc_final: 0.8683 (tpp) REVERT: C 98 ARG cc_start: 0.8548 (mtm110) cc_final: 0.7988 (mtm180) REVERT: C 148 TYR cc_start: 0.7766 (t80) cc_final: 0.7198 (t80) outliers start: 58 outliers final: 44 residues processed: 192 average time/residue: 0.1747 time to fit residues: 44.4177 Evaluate side-chains 188 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 143 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 16 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 89 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 251 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 56 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6465 Z= 0.249 Angle : 0.600 6.880 8817 Z= 0.311 Chirality : 0.041 0.130 1110 Planarity : 0.004 0.043 1095 Dihedral : 4.776 18.205 888 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 7.44 % Allowed : 21.35 % Favored : 71.21 % 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: 0.21 (0.28), residues: 834 helix: 0.06 (0.35), residues: 210 sheet: -0.87 (0.40), residues: 138 loop : 0.69 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 80 HIS 0.004 0.002 HIS B 127 PHE 0.025 0.002 PHE B 166 TYR 0.020 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 209 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 155 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8023 (mtm110) cc_final: 0.7541 (ptt-90) REVERT: A 41 LYS cc_start: 0.9239 (ttmm) cc_final: 0.8798 (tttp) REVERT: A 166 PHE cc_start: 0.9222 (t80) cc_final: 0.8956 (t80) REVERT: A 182 TYR cc_start: 0.7618 (p90) cc_final: 0.6796 (p90) REVERT: A 243 SER cc_start: 0.8711 (m) cc_final: 0.8477 (t) REVERT: B 8 ARG cc_start: 0.8346 (ttt-90) cc_final: 0.7779 (ttt180) REVERT: B 19 ARG cc_start: 0.7783 (mtm-85) cc_final: 0.7232 (ptt-90) REVERT: B 40 GLU cc_start: 0.8228 (pt0) cc_final: 0.7985 (pt0) REVERT: B 73 ASP cc_start: 0.8545 (t70) cc_final: 0.8006 (t0) REVERT: C 84 MET cc_start: 0.8925 (tpt) cc_final: 0.8644 (tpp) REVERT: C 98 ARG cc_start: 0.8527 (mtm110) cc_final: 0.7993 (mtm180) REVERT: C 148 TYR cc_start: 0.7539 (t80) cc_final: 0.6989 (t80) outliers start: 54 outliers final: 45 residues processed: 192 average time/residue: 0.1773 time to fit residues: 44.6023 Evaluate side-chains 190 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 145 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 45 THR Chi-restraints excluded: chain A residue 51 ASP 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 110 ASN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 251 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6465 Z= 0.281 Angle : 0.641 8.976 8817 Z= 0.331 Chirality : 0.041 0.134 1110 Planarity : 0.004 0.044 1095 Dihedral : 4.849 18.285 888 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 7.99 % Allowed : 21.35 % Favored : 70.66 % 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: -0.22 (0.34), residues: 216 sheet: -1.01 (0.40), residues: 138 loop : 0.67 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 80 HIS 0.005 0.002 HIS B 68 PHE 0.014 0.002 PHE A 50 TYR 0.024 0.002 TYR A 103 ARG 0.013 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 209 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 151 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8280 (tp) REVERT: A 19 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7670 (ptt-90) REVERT: A 41 LYS cc_start: 0.9248 (ttmm) cc_final: 0.8800 (tttp) REVERT: A 87 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7330 (tm-30) REVERT: A 166 PHE cc_start: 0.9239 (t80) cc_final: 0.8978 (t80) REVERT: A 182 TYR cc_start: 0.7607 (p90) cc_final: 0.6803 (p90) REVERT: A 243 SER cc_start: 0.8712 (m) cc_final: 0.8474 (t) REVERT: B 8 ARG cc_start: 0.8310 (ttt-90) cc_final: 0.7764 (ttt180) REVERT: B 19 ARG cc_start: 0.7841 (mtm-85) cc_final: 0.7506 (ptt-90) REVERT: B 73 ASP cc_start: 0.8614 (t70) cc_final: 0.8092 (t0) REVERT: B 101 MET cc_start: 0.8296 (mmm) cc_final: 0.8020 (mmm) REVERT: C 19 ARG cc_start: 0.8319 (mtm110) cc_final: 0.8103 (mtm110) REVERT: C 73 ASP cc_start: 0.8540 (m-30) cc_final: 0.8260 (t70) REVERT: C 84 MET cc_start: 0.8912 (tpt) cc_final: 0.8639 (tpp) REVERT: C 98 ARG cc_start: 0.8525 (mtm110) cc_final: 0.7952 (mtm180) REVERT: C 148 TYR cc_start: 0.7548 (t80) cc_final: 0.7010 (t80) outliers start: 58 outliers final: 52 residues processed: 194 average time/residue: 0.1657 time to fit residues: 42.5931 Evaluate side-chains 198 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 145 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 16 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 89 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 147 THR 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 195 ASN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 259 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6465 Z= 0.355 Angle : 0.688 10.279 8817 Z= 0.356 Chirality : 0.043 0.175 1110 Planarity : 0.004 0.044 1095 Dihedral : 5.103 20.297 888 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 8.68 % Allowed : 22.73 % Favored : 68.60 % 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: -0.24 (0.28), residues: 834 helix: -0.41 (0.34), residues: 213 sheet: -1.31 (0.42), residues: 120 loop : 0.44 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 80 HIS 0.005 0.002 HIS B 68 PHE 0.028 0.003 PHE B 166 TYR 0.025 0.003 TYR A 150 ARG 0.010 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 211 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 148 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8299 (tp) REVERT: A 19 ARG cc_start: 0.8124 (mtm110) cc_final: 0.7602 (ptt-90) REVERT: A 41 LYS cc_start: 0.9243 (ttmm) cc_final: 0.8855 (tttp) REVERT: A 87 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7439 (tm-30) REVERT: A 182 TYR cc_start: 0.7700 (p90) cc_final: 0.6833 (p90) REVERT: A 243 SER cc_start: 0.8729 (m) cc_final: 0.8480 (t) REVERT: B 8 ARG cc_start: 0.8374 (ttt-90) cc_final: 0.7798 (ttt180) REVERT: B 19 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7468 (ptt-90) REVERT: B 73 ASP cc_start: 0.8697 (t70) cc_final: 0.8189 (t0) REVERT: B 196 MET cc_start: 0.7458 (tpt) cc_final: 0.7232 (tpt) REVERT: C 84 MET cc_start: 0.8911 (tpt) cc_final: 0.8639 (tpp) REVERT: C 98 ARG cc_start: 0.8534 (mtm110) cc_final: 0.7832 (mtm180) REVERT: C 148 TYR cc_start: 0.7562 (t80) cc_final: 0.6970 (t80) outliers start: 63 outliers final: 59 residues processed: 194 average time/residue: 0.1638 time to fit residues: 42.2306 Evaluate side-chains 201 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 141 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU 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 57 ASN Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 16 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 89 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 147 THR 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 195 ASN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 251 THR 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 48 optimal weight: 10.0000 chunk 24 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 0.0980 chunk 70 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6465 Z= 0.163 Angle : 0.645 13.481 8817 Z= 0.323 Chirality : 0.042 0.187 1110 Planarity : 0.004 0.041 1095 Dihedral : 4.448 15.907 888 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 6.47 % Allowed : 24.79 % Favored : 68.73 % 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: -0.08 (0.35), residues: 213 sheet: -1.30 (0.40), residues: 135 loop : 0.62 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 80 HIS 0.002 0.001 HIS A 68 PHE 0.018 0.002 PHE A 166 TYR 0.021 0.002 TYR A 103 ARG 0.006 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 213 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 166 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8094 (mtm110) cc_final: 0.7747 (ptt-90) REVERT: A 41 LYS cc_start: 0.9207 (ttmm) cc_final: 0.8824 (tttp) REVERT: A 87 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7286 (tm-30) REVERT: A 98 ARG cc_start: 0.8427 (mtm180) cc_final: 0.8170 (mtm180) REVERT: A 182 TYR cc_start: 0.7607 (p90) cc_final: 0.6840 (p90) REVERT: A 243 SER cc_start: 0.8668 (m) cc_final: 0.8395 (t) REVERT: B 19 ARG cc_start: 0.7913 (mtm-85) cc_final: 0.7444 (ptt-90) REVERT: B 55 GLN cc_start: 0.8986 (pm20) cc_final: 0.8771 (pm20) REVERT: B 73 ASP cc_start: 0.8420 (t70) cc_final: 0.7857 (t0) REVERT: B 196 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7278 (tpt) REVERT: C 84 MET cc_start: 0.8861 (tpt) cc_final: 0.8591 (tpp) REVERT: C 98 ARG cc_start: 0.8521 (mtm110) cc_final: 0.7936 (mtm180) REVERT: C 125 LEU cc_start: 0.8863 (pp) cc_final: 0.8632 (pt) REVERT: C 148 TYR cc_start: 0.7499 (t80) cc_final: 0.6902 (t80) outliers start: 47 outliers final: 38 residues processed: 198 average time/residue: 0.1671 time to fit residues: 43.9156 Evaluate side-chains 190 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 151 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 147 THR 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 195 ASN Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 211 MET 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 75 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 0.0270 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6465 Z= 0.213 Angle : 0.663 12.676 8817 Z= 0.331 Chirality : 0.042 0.166 1110 Planarity : 0.004 0.041 1095 Dihedral : 4.534 21.602 888 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 6.34 % Allowed : 26.45 % Favored : 67.22 % 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: -0.07 (0.29), residues: 834 helix: -0.21 (0.35), residues: 213 sheet: -1.30 (0.41), residues: 135 loop : 0.61 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 80 HIS 0.003 0.001 HIS B 68 PHE 0.017 0.002 PHE A 82 TYR 0.021 0.002 TYR A 281 ARG 0.010 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 202 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 156 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8220 (mtm110) cc_final: 0.7758 (ptt-90) REVERT: A 41 LYS cc_start: 0.9223 (ttmm) cc_final: 0.8832 (tttp) REVERT: A 49 MET cc_start: 0.8729 (mmp) cc_final: 0.8373 (mmp) REVERT: A 87 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7404 (tm-30) REVERT: A 98 ARG cc_start: 0.8507 (mtm180) cc_final: 0.8174 (mtm180) REVERT: A 182 TYR cc_start: 0.7594 (p90) cc_final: 0.6846 (p90) REVERT: A 243 SER cc_start: 0.8758 (m) cc_final: 0.8485 (t) REVERT: B 8 ARG cc_start: 0.8627 (ptm160) cc_final: 0.8034 (ttt180) REVERT: B 19 ARG cc_start: 0.7915 (mtm-85) cc_final: 0.7426 (ptt-90) REVERT: B 73 ASP cc_start: 0.8474 (t70) cc_final: 0.7996 (t0) REVERT: B 196 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7299 (tpt) REVERT: C 84 MET cc_start: 0.8881 (tpt) cc_final: 0.8602 (tpp) REVERT: C 95 VAL cc_start: 0.9599 (t) cc_final: 0.9312 (p) REVERT: C 98 ARG cc_start: 0.8541 (mtm110) cc_final: 0.8077 (mtm180) REVERT: C 125 LEU cc_start: 0.8841 (pp) cc_final: 0.8606 (pt) REVERT: C 148 TYR cc_start: 0.7539 (t80) cc_final: 0.6957 (t80) outliers start: 46 outliers final: 40 residues processed: 186 average time/residue: 0.1845 time to fit residues: 45.6393 Evaluate side-chains 192 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 151 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 116 TYR 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 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 147 THR 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 195 ASN Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 259 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 52 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6465 Z= 0.196 Angle : 0.677 13.162 8817 Z= 0.335 Chirality : 0.042 0.171 1110 Planarity : 0.004 0.040 1095 Dihedral : 4.478 22.433 888 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 5.79 % Allowed : 26.86 % Favored : 67.36 % 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: -0.09 (0.29), residues: 834 helix: -0.28 (0.35), residues: 213 sheet: -1.24 (0.40), residues: 135 loop : 0.61 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 80 HIS 0.002 0.001 HIS B 68 PHE 0.035 0.002 PHE B 166 TYR 0.021 0.002 TYR A 103 ARG 0.016 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 200 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 158 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7776 (ptt-90) REVERT: A 41 LYS cc_start: 0.9217 (ttmm) cc_final: 0.8828 (tttp) REVERT: A 49 MET cc_start: 0.8727 (mmp) cc_final: 0.8369 (mmp) REVERT: A 87 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7625 (tm-30) REVERT: A 98 ARG cc_start: 0.8474 (mtm180) cc_final: 0.8133 (mtm180) REVERT: A 182 TYR cc_start: 0.7571 (p90) cc_final: 0.6862 (p90) REVERT: A 230 TYR cc_start: 0.7951 (t80) cc_final: 0.7657 (t80) REVERT: A 243 SER cc_start: 0.8719 (m) cc_final: 0.8464 (t) REVERT: B 8 ARG cc_start: 0.8597 (ptm160) cc_final: 0.7998 (mtt180) REVERT: B 19 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7392 (ptt-90) REVERT: B 55 GLN cc_start: 0.9023 (pm20) cc_final: 0.8764 (pm20) REVERT: B 73 ASP cc_start: 0.8450 (t70) cc_final: 0.7890 (t0) REVERT: C 84 MET cc_start: 0.8868 (tpt) cc_final: 0.8586 (tpp) REVERT: C 95 VAL cc_start: 0.9600 (t) cc_final: 0.9305 (p) REVERT: C 98 ARG cc_start: 0.8545 (mtm110) cc_final: 0.8049 (mtm180) REVERT: C 125 LEU cc_start: 0.8840 (pp) cc_final: 0.8635 (pt) REVERT: C 148 TYR cc_start: 0.7519 (t80) cc_final: 0.6857 (t80) REVERT: C 230 TYR cc_start: 0.8256 (t80) cc_final: 0.7764 (t80) outliers start: 42 outliers final: 40 residues processed: 186 average time/residue: 0.1837 time to fit residues: 45.1349 Evaluate side-chains 192 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 152 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 116 TYR 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 224 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 147 THR 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 195 ASN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 259 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 68 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.099028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.083463 restraints weight = 19921.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.085949 restraints weight = 10364.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.087569 restraints weight = 6839.822| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6465 Z= 0.172 Angle : 0.684 13.545 8817 Z= 0.334 Chirality : 0.042 0.160 1110 Planarity : 0.004 0.039 1095 Dihedral : 4.288 21.133 888 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 5.51 % Allowed : 27.27 % Favored : 67.22 % 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: -0.21 (0.35), residues: 210 sheet: -1.17 (0.40), residues: 135 loop : 0.64 (0.29), residues: 489 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 0.033 0.002 PHE B 166 TYR 0.034 0.002 TYR A 148 ARG 0.010 0.001 ARG C 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1613.42 seconds wall clock time: 29 minutes 34.01 seconds (1774.01 seconds total)