Starting phenix.real_space_refine on Wed Mar 4 01:40:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ysl_10899/03_2026/6ysl_10899.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ysl_10899/03_2026/6ysl_10899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ysl_10899/03_2026/6ysl_10899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ysl_10899/03_2026/6ysl_10899.map" model { file = "/net/cci-nas-00/data/ceres_data/6ysl_10899/03_2026/6ysl_10899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ysl_10899/03_2026/6ysl_10899.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 40 5.16 5 C 6595 2.51 5 N 1646 2.21 5 O 1847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10128 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "A" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 208 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "B" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 201 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "F" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "E" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1947 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "D" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1947 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "C" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1947 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Time building chain proxies: 2.34, per 1000 atoms: 0.23 Number of scatterers: 10128 At special positions: 0 Unit cell: (96.996, 110.97, 94.53, 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 40 16.00 O 1847 8.00 N 1646 7.00 C 6595 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 602.4 milliseconds 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2478 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 0 sheets defined 75.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'G' and resid 3 through 24 removed outlier: 4.157A pdb=" N ILE G 7 " --> pdb=" O LYS G 3 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 51 Processing helix chain 'G' and resid 58 through 64 Processing helix chain 'G' and resid 74 through 79 removed outlier: 4.163A pdb=" N ILE G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 93 removed outlier: 3.509A pdb=" N ARG G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU G 92 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 117 removed outlier: 3.682A pdb=" N LYS G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY G 112 " --> pdb=" O PHE G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 170 removed outlier: 4.078A pdb=" N ARG G 126 " --> pdb=" O ALA G 122 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE G 128 " --> pdb=" O PHE G 124 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE G 146 " --> pdb=" O ALA G 142 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE G 147 " --> pdb=" O GLY G 143 " (cutoff:3.500A) Proline residue: G 155 - end of helix Processing helix chain 'G' and resid 177 through 199 removed outlier: 3.609A pdb=" N HIS G 181 " --> pdb=" O ASP G 177 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE G 183 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR G 190 " --> pdb=" O ALA G 186 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY G 197 " --> pdb=" O GLY G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 232 removed outlier: 3.879A pdb=" N MET G 222 " --> pdb=" O LEU G 218 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE G 223 " --> pdb=" O ARG G 219 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU G 224 " --> pdb=" O GLU G 220 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY G 225 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL G 229 " --> pdb=" O GLY G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 243 Processing helix chain 'G' and resid 247 through 252 removed outlier: 3.765A pdb=" N LEU G 252 " --> pdb=" O ALA G 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 37 removed outlier: 3.697A pdb=" N TYR A 22 " --> pdb=" O TRP A 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 37 Processing helix chain 'F' and resid 5 through 22 removed outlier: 3.748A pdb=" N LEU F 11 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 51 removed outlier: 4.288A pdb=" N ILE F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE F 44 " --> pdb=" O ILE F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 66 removed outlier: 3.540A pdb=" N LEU F 62 " --> pdb=" O LYS F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 77 Processing helix chain 'F' and resid 78 through 92 removed outlier: 4.886A pdb=" N GLU F 84 " --> pdb=" O PRO F 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TRP F 85 " --> pdb=" O MET F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 100 removed outlier: 3.738A pdb=" N SER F 100 " --> pdb=" O LEU F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 114 Processing helix chain 'F' and resid 115 through 118 Processing helix chain 'F' and resid 124 through 171 removed outlier: 3.639A pdb=" N GLY F 143 " --> pdb=" O ARG F 139 " (cutoff:3.500A) Proline residue: F 155 - end of helix Processing helix chain 'F' and resid 179 through 196 removed outlier: 5.268A pdb=" N ALA F 185 " --> pdb=" O HIS F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 232 removed outlier: 3.509A pdb=" N LEU F 230 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU F 231 " --> pdb=" O LEU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 240 removed outlier: 3.554A pdb=" N GLN F 240 " --> pdb=" O VAL F 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 24 removed outlier: 4.068A pdb=" N LEU E 22 " --> pdb=" O VAL E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 51 removed outlier: 3.560A pdb=" N ILE E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE E 44 " --> pdb=" O ILE E 40 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA E 50 " --> pdb=" O ALA E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 64 Processing helix chain 'E' and resid 74 through 78 Processing helix chain 'E' and resid 84 through 89 Processing helix chain 'E' and resid 97 through 102 removed outlier: 3.734A pdb=" N ILE E 101 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 102' Processing helix chain 'E' and resid 109 through 119 removed outlier: 4.505A pdb=" N MET E 115 " --> pdb=" O ASN E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 172 removed outlier: 3.946A pdb=" N ILE E 146 " --> pdb=" O ALA E 142 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) Proline residue: E 155 - end of helix removed outlier: 3.839A pdb=" N ILE E 164 " --> pdb=" O LEU E 160 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HIS E 172 " --> pdb=" O ALA E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 199 removed outlier: 3.757A pdb=" N HIS E 181 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU E 191 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY E 197 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL E 199 " --> pdb=" O PHE E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 230 Processing helix chain 'E' and resid 234 through 242 Processing helix chain 'E' and resid 243 through 246 removed outlier: 3.678A pdb=" N LEU E 246 " --> pdb=" O LEU E 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 243 through 246' Processing helix chain 'E' and resid 248 through 254 removed outlier: 3.671A pdb=" N LEU E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS E 253 " --> pdb=" O LYS E 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 23 removed outlier: 4.074A pdb=" N GLY D 8 " --> pdb=" O THR D 4 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 51 removed outlier: 3.707A pdb=" N ILE D 36 " --> pdb=" O ASN D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 66 removed outlier: 3.854A pdb=" N VAL D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 removed outlier: 3.580A pdb=" N ILE D 79 " --> pdb=" O GLU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 91 removed outlier: 3.668A pdb=" N LEU D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 118 Processing helix chain 'D' and resid 125 through 170 removed outlier: 3.891A pdb=" N MET D 129 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N PHE D 147 " --> pdb=" O GLY D 143 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) Proline residue: D 155 - end of helix Processing helix chain 'D' and resid 181 through 199 removed outlier: 3.791A pdb=" N ALA D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 230 Processing helix chain 'D' and resid 235 through 242 removed outlier: 4.086A pdb=" N GLN D 240 " --> pdb=" O LYS D 236 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 242 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'D' and resid 249 through 254 removed outlier: 4.333A pdb=" N LYS D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE D 254 " --> pdb=" O ASP D 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 249 through 254' Processing helix chain 'C' and resid 4 through 21 Processing helix chain 'C' and resid 27 through 31 removed outlier: 3.815A pdb=" N LEU C 30 " --> pdb=" O PHE C 27 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA C 31 " --> pdb=" O SER C 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 27 through 31' Processing helix chain 'C' and resid 34 through 51 Processing helix chain 'C' and resid 55 through 57 No H-bonds generated for 'chain 'C' and resid 55 through 57' Processing helix chain 'C' and resid 58 through 66 Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 84 through 92 removed outlier: 3.675A pdb=" N GLU C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 101 removed outlier: 4.264A pdb=" N SER C 100 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE C 101 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 118 Processing helix chain 'C' and resid 123 through 171 removed outlier: 4.005A pdb=" N ILE C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Proline residue: C 155 - end of helix Processing helix chain 'C' and resid 177 through 186 removed outlier: 3.626A pdb=" N ALA C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 199 removed outlier: 3.695A pdb=" N LEU C 191 " --> pdb=" O PHE C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 230 Processing helix chain 'C' and resid 237 through 243 Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 252 648 hydrogen bonds defined for protein. 1917 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: 1.49 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3055 1.34 - 1.46: 1453 1.46 - 1.57: 5705 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 10293 Sorted by residual: bond pdb=" C ILE F 79 " pdb=" N PRO F 80 " ideal model delta sigma weight residual 1.334 1.383 -0.049 8.40e-03 1.42e+04 3.44e+01 bond pdb=" C ALA E 154 " pdb=" N PRO E 155 " ideal model delta sigma weight residual 1.336 1.373 -0.038 1.23e-02 6.61e+03 9.49e+00 bond pdb=" C VAL E 59 " pdb=" N PRO E 60 " ideal model delta sigma weight residual 1.336 1.372 -0.036 1.20e-02 6.94e+03 9.13e+00 bond pdb=" N GLU B 16 " pdb=" CA GLU B 16 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.31e-02 5.83e+03 6.66e+00 bond pdb=" N ASP A 15 " pdb=" CA ASP A 15 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.17e-02 7.31e+03 5.94e+00 ... (remaining 10288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 13345 2.51 - 5.02: 456 5.02 - 7.54: 95 7.54 - 10.05: 28 10.05 - 12.56: 7 Bond angle restraints: 13931 Sorted by residual: angle pdb=" C LEU C 78 " pdb=" N ILE C 79 " pdb=" CA ILE C 79 " ideal model delta sigma weight residual 120.24 124.27 -4.03 6.30e-01 2.52e+00 4.09e+01 angle pdb=" N GLU E 84 " pdb=" CA GLU E 84 " pdb=" C GLU E 84 " ideal model delta sigma weight residual 113.43 106.49 6.94 1.26e+00 6.30e-01 3.03e+01 angle pdb=" N ASN E 32 " pdb=" CA ASN E 32 " pdb=" C ASN E 32 " ideal model delta sigma weight residual 109.81 120.95 -11.14 2.21e+00 2.05e-01 2.54e+01 angle pdb=" C GLU G 102 " pdb=" N ASP G 103 " pdb=" CA ASP G 103 " ideal model delta sigma weight residual 121.54 131.14 -9.60 1.91e+00 2.74e-01 2.53e+01 angle pdb=" C VAL G 117 " pdb=" N ASP G 118 " pdb=" CA ASP G 118 " ideal model delta sigma weight residual 121.54 130.75 -9.21 1.91e+00 2.74e-01 2.33e+01 ... (remaining 13926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 5659 15.00 - 30.00: 410 30.00 - 45.00: 145 45.00 - 60.00: 8 60.00 - 75.00: 6 Dihedral angle restraints: 6228 sinusoidal: 2414 harmonic: 3814 Sorted by residual: dihedral pdb=" CA ALA F 234 " pdb=" C ALA F 234 " pdb=" N PRO F 235 " pdb=" CA PRO F 235 " ideal model delta harmonic sigma weight residual -180.00 -151.59 -28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA HIS F 181 " pdb=" C HIS F 181 " pdb=" N ALA F 182 " pdb=" CA ALA F 182 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ASN G 32 " pdb=" C ASN G 32 " pdb=" N PRO G 33 " pdb=" CA PRO G 33 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 6225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1227 0.060 - 0.120: 370 0.120 - 0.180: 85 0.180 - 0.240: 11 0.240 - 0.301: 1 Chirality restraints: 1694 Sorted by residual: chirality pdb=" CA ASN E 32 " pdb=" N ASN E 32 " pdb=" C ASN E 32 " pdb=" CB ASN E 32 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE D 7 " pdb=" CA ILE D 7 " pdb=" CG1 ILE D 7 " pdb=" CG2 ILE D 7 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASP G 118 " pdb=" N ASP G 118 " pdb=" C ASP G 118 " pdb=" CB ASP G 118 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1691 not shown) Planarity restraints: 1736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 197 " 0.021 2.00e-02 2.50e+03 4.24e-02 1.79e+01 pdb=" C GLY F 197 " -0.073 2.00e-02 2.50e+03 pdb=" O GLY F 197 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR F 198 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 204 " -0.012 2.00e-02 2.50e+03 1.89e-02 6.27e+00 pdb=" CG PHE E 204 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE E 204 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE E 204 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE E 204 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 204 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE E 204 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 124 " -0.023 2.00e-02 2.50e+03 1.82e-02 5.82e+00 pdb=" CG PHE C 124 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE C 124 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 124 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 124 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 124 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 124 " -0.007 2.00e-02 2.50e+03 ... (remaining 1733 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1761 2.77 - 3.30: 10211 3.30 - 3.83: 16641 3.83 - 4.37: 19622 4.37 - 4.90: 32248 Nonbonded interactions: 80483 Sorted by model distance: nonbonded pdb=" O LEU E 192 " pdb=" OG1 THR E 196 " model vdw 2.232 3.040 nonbonded pdb=" OE2 GLU B 16 " pdb=" OH TYR C 198 " model vdw 2.234 3.040 nonbonded pdb=" O LEU F 192 " pdb=" OG1 THR F 196 " model vdw 2.235 3.040 nonbonded pdb=" O GLY F 180 " pdb=" OG SER F 184 " model vdw 2.282 3.040 nonbonded pdb=" O ILE G 39 " pdb=" OG1 THR G 43 " model vdw 2.286 3.040 ... (remaining 80478 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 15 through 39) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 3 through 256) selection = (chain 'D' and resid 3 through 256) selection = (chain 'E' and resid 3 through 256) selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.330 Find NCS groups from input model: 0.190 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 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 : 0.006 0.087 10293 Z= 0.280 Angle : 1.169 12.558 13931 Z= 0.607 Chirality : 0.060 0.301 1694 Planarity : 0.008 0.059 1736 Dihedral : 12.213 74.996 3750 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.01 % Favored : 90.92 % Rotamer: Outliers : 0.47 % Allowed : 6.93 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.73 (0.18), residues: 1310 helix: -2.77 (0.13), residues: 942 sheet: None (None), residues: 0 loop : -3.60 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 210 TYR 0.027 0.005 TYR G 153 PHE 0.043 0.003 PHE E 204 TRP 0.030 0.003 TRP C 201 HIS 0.013 0.003 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00606 (10293) covalent geometry : angle 1.16896 (13931) hydrogen bonds : bond 0.14638 ( 648) hydrogen bonds : angle 7.77303 ( 1917) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 433 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 20 MET cc_start: 0.7364 (mmt) cc_final: 0.7094 (mmm) REVERT: G 68 LYS cc_start: 0.7129 (ttmt) cc_final: 0.6446 (tppt) REVERT: G 136 MET cc_start: 0.7955 (tmm) cc_final: 0.7527 (ttm) REVERT: G 139 ARG cc_start: 0.7549 (ttm110) cc_final: 0.6695 (ttt-90) REVERT: G 219 ARG cc_start: 0.8460 (mtp85) cc_final: 0.8153 (mtp85) REVERT: G 221 VAL cc_start: 0.9235 (p) cc_final: 0.8962 (p) REVERT: G 224 GLU cc_start: 0.8435 (mp0) cc_final: 0.8168 (mp0) REVERT: B 20 VAL cc_start: 0.8659 (t) cc_final: 0.8352 (m) REVERT: F 84 GLU cc_start: 0.6442 (pp20) cc_final: 0.6168 (pm20) REVERT: F 125 ILE cc_start: 0.7587 (mm) cc_final: 0.7383 (tp) REVERT: F 176 THR cc_start: 0.8083 (t) cc_final: 0.7858 (m) REVERT: F 204 PHE cc_start: 0.7942 (m-10) cc_final: 0.7607 (m-80) REVERT: F 219 ARG cc_start: 0.8276 (mtt-85) cc_final: 0.7443 (mtt-85) REVERT: F 226 VAL cc_start: 0.9491 (p) cc_final: 0.9106 (m) REVERT: F 241 LYS cc_start: 0.6418 (pttt) cc_final: 0.6149 (pttp) REVERT: F 244 MET cc_start: 0.7025 (ptt) cc_final: 0.6799 (ptt) REVERT: E 87 GLN cc_start: 0.6902 (tm-30) cc_final: 0.6691 (tm-30) REVERT: E 129 MET cc_start: 0.8204 (tpp) cc_final: 0.7619 (mtp) REVERT: E 134 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8087 (mm-30) REVERT: E 179 LEU cc_start: 0.7621 (tt) cc_final: 0.7276 (pp) REVERT: E 217 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8462 (tptt) REVERT: D 6 LEU cc_start: 0.7847 (pt) cc_final: 0.7074 (tp) REVERT: D 81 MET cc_start: 0.5785 (tpp) cc_final: 0.5567 (tmm) REVERT: D 85 TRP cc_start: 0.6760 (p90) cc_final: 0.6406 (p90) REVERT: D 181 HIS cc_start: 0.4848 (p90) cc_final: 0.3915 (m170) REVERT: D 210 ARG cc_start: 0.8742 (mmt180) cc_final: 0.8010 (tmm160) REVERT: D 244 MET cc_start: 0.6536 (mpt) cc_final: 0.5761 (mtp) REVERT: C 72 GLN cc_start: 0.6937 (pp30) cc_final: 0.6672 (tt0) REVERT: C 87 GLN cc_start: 0.6396 (mm-40) cc_final: 0.5983 (tp-100) REVERT: C 127 ASP cc_start: 0.7381 (p0) cc_final: 0.6140 (p0) REVERT: C 181 HIS cc_start: 0.6826 (t-170) cc_final: 0.6616 (t70) REVERT: C 198 TYR cc_start: 0.6937 (m-10) cc_final: 0.6611 (m-80) outliers start: 5 outliers final: 3 residues processed: 437 average time/residue: 0.1028 time to fit residues: 61.9994 Evaluate side-chains 263 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 260 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 16 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 87 GLN G 140 HIS G 172 HIS G 202 HIS ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN F 140 HIS F 206 ASN E 140 HIS E 141 GLN E 206 ASN D 140 HIS D 175 ASN D 206 ASN C 32 ASN C 87 GLN C 149 GLN C 172 HIS C 202 HIS ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.174755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.144094 restraints weight = 17170.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.146661 restraints weight = 11197.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.148415 restraints weight = 8551.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.149217 restraints weight = 7242.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.150004 restraints weight = 6636.868| |-----------------------------------------------------------------------------| r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10293 Z= 0.154 Angle : 0.796 8.679 13931 Z= 0.401 Chirality : 0.045 0.183 1694 Planarity : 0.005 0.044 1736 Dihedral : 6.724 60.138 1383 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 4.03 % Allowed : 17.32 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.21), residues: 1310 helix: -1.31 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -3.35 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 91 TYR 0.017 0.002 TYR C 153 PHE 0.041 0.002 PHE C 124 TRP 0.014 0.002 TRP E 201 HIS 0.004 0.001 HIS F 202 Details of bonding type rmsd covalent geometry : bond 0.00343 (10293) covalent geometry : angle 0.79613 (13931) hydrogen bonds : bond 0.03863 ( 648) hydrogen bonds : angle 5.13990 ( 1917) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 294 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 LYS cc_start: 0.7149 (ttmt) cc_final: 0.6605 (mmtm) REVERT: G 125 ILE cc_start: 0.7807 (mm) cc_final: 0.7529 (mm) REVERT: G 221 VAL cc_start: 0.8961 (p) cc_final: 0.8740 (p) REVERT: F 131 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7194 (mp0) REVERT: F 204 PHE cc_start: 0.7856 (m-10) cc_final: 0.7334 (m-80) REVERT: F 241 LYS cc_start: 0.6479 (pttt) cc_final: 0.6037 (pttp) REVERT: E 103 ASP cc_start: 0.4792 (t70) cc_final: 0.4374 (t70) REVERT: E 208 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6261 (mt) REVERT: D 6 LEU cc_start: 0.7552 (pt) cc_final: 0.7192 (tp) REVERT: D 210 ARG cc_start: 0.8406 (mmt180) cc_final: 0.8137 (tmm160) REVERT: D 244 MET cc_start: 0.6161 (mpt) cc_final: 0.5342 (mtp) outliers start: 43 outliers final: 18 residues processed: 323 average time/residue: 0.0875 time to fit residues: 40.7043 Evaluate side-chains 272 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 253 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 63 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 126 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 GLN F 120 GLN F 206 ASN E 141 GLN D 206 ASN ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.173663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.142826 restraints weight = 17317.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.145421 restraints weight = 11235.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.147075 restraints weight = 8509.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.147699 restraints weight = 7221.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.148642 restraints weight = 6659.641| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10293 Z= 0.151 Angle : 0.776 12.894 13931 Z= 0.382 Chirality : 0.044 0.197 1694 Planarity : 0.004 0.043 1736 Dihedral : 5.741 26.916 1376 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 4.49 % Allowed : 21.07 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.22), residues: 1310 helix: -0.82 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -3.27 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 251 TYR 0.011 0.002 TYR B 22 PHE 0.025 0.002 PHE G 195 TRP 0.020 0.002 TRP D 85 HIS 0.003 0.001 HIS F 202 Details of bonding type rmsd covalent geometry : bond 0.00345 (10293) covalent geometry : angle 0.77608 (13931) hydrogen bonds : bond 0.03714 ( 648) hydrogen bonds : angle 4.83674 ( 1917) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 273 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 LYS cc_start: 0.7257 (ttmt) cc_final: 0.6686 (mmtm) REVERT: F 131 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7299 (mt-10) REVERT: F 241 LYS cc_start: 0.6364 (pttt) cc_final: 0.5997 (pttp) REVERT: E 103 ASP cc_start: 0.5001 (t70) cc_final: 0.4661 (t70) REVERT: E 208 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.6398 (mt) REVERT: E 244 MET cc_start: 0.6063 (tpt) cc_final: 0.5739 (tpp) REVERT: D 6 LEU cc_start: 0.7562 (pt) cc_final: 0.7251 (tp) REVERT: D 81 MET cc_start: 0.5417 (tpp) cc_final: 0.5154 (tpt) REVERT: D 210 ARG cc_start: 0.8386 (mmt180) cc_final: 0.8018 (tmm160) REVERT: D 222 MET cc_start: 0.6870 (mtt) cc_final: 0.6652 (mtt) REVERT: D 244 MET cc_start: 0.6155 (mpt) cc_final: 0.5394 (mtp) REVERT: C 72 GLN cc_start: 0.6571 (pm20) cc_final: 0.6213 (pp30) outliers start: 48 outliers final: 21 residues processed: 307 average time/residue: 0.0780 time to fit residues: 36.0146 Evaluate side-chains 253 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 231 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 172 HIS Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 63 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 61 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 113 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 GLN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.174434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.143760 restraints weight = 17552.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.146367 restraints weight = 11367.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.148106 restraints weight = 8615.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.149104 restraints weight = 7267.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.149766 restraints weight = 6600.165| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10293 Z= 0.145 Angle : 0.768 11.923 13931 Z= 0.376 Chirality : 0.045 0.257 1694 Planarity : 0.004 0.041 1736 Dihedral : 5.448 26.641 1376 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.75 % Allowed : 21.91 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.23), residues: 1310 helix: -0.53 (0.16), residues: 957 sheet: None (None), residues: 0 loop : -3.23 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 251 TYR 0.015 0.002 TYR B 22 PHE 0.027 0.002 PHE E 195 TRP 0.017 0.001 TRP D 85 HIS 0.004 0.001 HIS D 181 Details of bonding type rmsd covalent geometry : bond 0.00336 (10293) covalent geometry : angle 0.76785 (13931) hydrogen bonds : bond 0.03503 ( 648) hydrogen bonds : angle 4.64360 ( 1917) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 268 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 LYS cc_start: 0.7263 (ttmt) cc_final: 0.6669 (mmtm) REVERT: G 130 THR cc_start: 0.8394 (m) cc_final: 0.8103 (p) REVERT: F 20 MET cc_start: 0.5484 (tpt) cc_final: 0.4665 (tpt) REVERT: F 131 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7322 (mt-10) REVERT: F 241 LYS cc_start: 0.6367 (pttt) cc_final: 0.6024 (pttp) REVERT: E 61 THR cc_start: 0.7575 (p) cc_final: 0.7159 (m) REVERT: E 208 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.6467 (mt) REVERT: E 244 MET cc_start: 0.5957 (tpt) cc_final: 0.5682 (tpp) REVERT: D 6 LEU cc_start: 0.7540 (pt) cc_final: 0.7265 (tp) REVERT: D 210 ARG cc_start: 0.8321 (mmt180) cc_final: 0.8060 (tmm160) REVERT: D 244 MET cc_start: 0.6048 (mpt) cc_final: 0.5256 (mtp) REVERT: C 72 GLN cc_start: 0.6614 (pm20) cc_final: 0.6135 (pp30) outliers start: 40 outliers final: 27 residues processed: 295 average time/residue: 0.0806 time to fit residues: 35.3015 Evaluate side-chains 267 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 208 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 83 optimal weight: 0.7980 chunk 78 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 GLN F 206 ASN E 141 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.175630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.145410 restraints weight = 17222.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.148121 restraints weight = 11042.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.149463 restraints weight = 8303.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.150818 restraints weight = 7108.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.151363 restraints weight = 6380.571| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 10293 Z= 0.142 Angle : 0.762 11.396 13931 Z= 0.374 Chirality : 0.044 0.185 1694 Planarity : 0.004 0.042 1736 Dihedral : 5.310 26.498 1376 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.40 % Allowed : 24.91 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.23), residues: 1310 helix: -0.28 (0.17), residues: 944 sheet: None (None), residues: 0 loop : -3.04 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 251 TYR 0.014 0.002 TYR F 153 PHE 0.026 0.002 PHE E 195 TRP 0.014 0.001 TRP F 85 HIS 0.004 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00324 (10293) covalent geometry : angle 0.76154 (13931) hydrogen bonds : bond 0.03470 ( 648) hydrogen bonds : angle 4.53273 ( 1917) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 264 time to evaluate : 0.397 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: G 68 LYS cc_start: 0.7282 (ttmt) cc_final: 0.6759 (mmtm) REVERT: G 130 THR cc_start: 0.8248 (m) cc_final: 0.7994 (p) REVERT: F 131 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7330 (mt-10) REVERT: F 208 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7317 (mm) REVERT: F 241 LYS cc_start: 0.6358 (pttt) cc_final: 0.5984 (pttp) REVERT: E 61 THR cc_start: 0.7503 (p) cc_final: 0.7191 (m) REVERT: E 87 GLN cc_start: 0.6197 (tm-30) cc_final: 0.5984 (tm-30) REVERT: E 208 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.6450 (mt) REVERT: D 6 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7263 (tp) REVERT: D 11 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.6288 (tt) REVERT: D 20 MET cc_start: 0.7135 (mmm) cc_final: 0.6572 (tpp) REVERT: D 244 MET cc_start: 0.5907 (mpt) cc_final: 0.5083 (mtp) REVERT: C 208 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7165 (mm) outliers start: 47 outliers final: 23 residues processed: 297 average time/residue: 0.0827 time to fit residues: 36.3527 Evaluate side-chains 267 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 172 HIS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 208 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 61 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 GLN F 206 ASN E 141 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 HIS ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.172132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.140824 restraints weight = 17390.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.143373 restraints weight = 11404.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.144997 restraints weight = 8741.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.145754 restraints weight = 7474.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.146632 restraints weight = 6876.199| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10293 Z= 0.175 Angle : 0.780 9.680 13931 Z= 0.390 Chirality : 0.046 0.267 1694 Planarity : 0.004 0.042 1736 Dihedral : 5.335 26.522 1376 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.59 % Allowed : 25.47 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.23), residues: 1310 helix: -0.21 (0.17), residues: 944 sheet: None (None), residues: 0 loop : -3.07 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 251 TYR 0.015 0.002 TYR F 153 PHE 0.029 0.002 PHE E 195 TRP 0.019 0.002 TRP F 85 HIS 0.004 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00415 (10293) covalent geometry : angle 0.77954 (13931) hydrogen bonds : bond 0.03642 ( 648) hydrogen bonds : angle 4.65521 ( 1917) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 0.358 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: G 68 LYS cc_start: 0.7361 (ttmt) cc_final: 0.6761 (mmtm) REVERT: G 129 MET cc_start: 0.7411 (mpp) cc_final: 0.7046 (mpp) REVERT: G 130 THR cc_start: 0.8269 (m) cc_final: 0.8003 (p) REVERT: F 208 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7186 (mm) REVERT: F 241 LYS cc_start: 0.6540 (pttt) cc_final: 0.6172 (pttp) REVERT: E 61 THR cc_start: 0.7585 (p) cc_final: 0.7323 (m) REVERT: E 81 MET cc_start: 0.7546 (ppp) cc_final: 0.7274 (ppp) REVERT: E 192 LEU cc_start: 0.7758 (mm) cc_final: 0.7180 (tp) REVERT: E 198 TYR cc_start: 0.6561 (OUTLIER) cc_final: 0.6337 (m-80) REVERT: E 208 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.6815 (mt) REVERT: E 244 MET cc_start: 0.5990 (tpt) cc_final: 0.5641 (tpp) REVERT: D 6 LEU cc_start: 0.7567 (pt) cc_final: 0.7241 (tp) REVERT: D 11 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6296 (tt) REVERT: D 244 MET cc_start: 0.5994 (mpt) cc_final: 0.5000 (mtp) REVERT: C 72 GLN cc_start: 0.6673 (pm20) cc_final: 0.6092 (pp30) outliers start: 49 outliers final: 30 residues processed: 290 average time/residue: 0.0802 time to fit residues: 34.3511 Evaluate side-chains 273 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 172 HIS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 166 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 73 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 60 optimal weight: 0.0570 chunk 37 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 GLN F 72 GLN F 206 ASN E 141 GLN E 214 GLN ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.175700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.144911 restraints weight = 17290.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.147518 restraints weight = 11294.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.149293 restraints weight = 8617.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.150398 restraints weight = 7293.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.150611 restraints weight = 6608.737| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 10293 Z= 0.142 Angle : 0.767 9.919 13931 Z= 0.383 Chirality : 0.045 0.270 1694 Planarity : 0.004 0.045 1736 Dihedral : 5.222 25.886 1376 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.56 % Allowed : 27.15 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.23), residues: 1310 helix: -0.08 (0.17), residues: 935 sheet: None (None), residues: 0 loop : -3.04 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 251 TYR 0.017 0.002 TYR A 22 PHE 0.027 0.002 PHE E 195 TRP 0.031 0.002 TRP F 85 HIS 0.005 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00318 (10293) covalent geometry : angle 0.76742 (13931) hydrogen bonds : bond 0.03570 ( 648) hydrogen bonds : angle 4.58386 ( 1917) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 265 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 LYS cc_start: 0.7308 (ttmt) cc_final: 0.6748 (mmtm) REVERT: G 129 MET cc_start: 0.7340 (mpp) cc_final: 0.7119 (mpp) REVERT: G 130 THR cc_start: 0.8276 (m) cc_final: 0.8018 (p) REVERT: F 85 TRP cc_start: 0.7225 (m-10) cc_final: 0.6971 (m-10) REVERT: F 131 GLU cc_start: 0.7665 (mt-10) cc_final: 0.6963 (mp0) REVERT: F 208 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7347 (mm) REVERT: F 241 LYS cc_start: 0.6493 (pttt) cc_final: 0.6108 (pttp) REVERT: E 61 THR cc_start: 0.7527 (p) cc_final: 0.7323 (m) REVERT: E 81 MET cc_start: 0.7591 (ppp) cc_final: 0.7325 (ppp) REVERT: E 131 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7403 (pt0) REVERT: E 198 TYR cc_start: 0.6518 (OUTLIER) cc_final: 0.6203 (m-80) REVERT: E 208 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.6837 (mt) REVERT: E 244 MET cc_start: 0.5912 (tpt) cc_final: 0.5586 (tpp) REVERT: D 6 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7203 (tp) REVERT: D 11 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.6225 (tt) REVERT: D 20 MET cc_start: 0.7099 (mmm) cc_final: 0.6521 (tpp) REVERT: C 217 LYS cc_start: 0.8248 (mmtt) cc_final: 0.8044 (mmmt) outliers start: 38 outliers final: 25 residues processed: 287 average time/residue: 0.0829 time to fit residues: 35.1707 Evaluate side-chains 273 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 243 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 172 HIS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 166 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 206 ASN G 240 GLN F 72 GLN F 120 GLN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 HIS ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.174352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.143275 restraints weight = 17307.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.145856 restraints weight = 11301.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.147569 restraints weight = 8665.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.148311 restraints weight = 7345.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.148829 restraints weight = 6751.844| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 10293 Z= 0.150 Angle : 0.794 15.373 13931 Z= 0.392 Chirality : 0.046 0.306 1694 Planarity : 0.004 0.043 1736 Dihedral : 5.127 25.940 1376 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.12 % Allowed : 27.34 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.23), residues: 1310 helix: -0.02 (0.17), residues: 941 sheet: None (None), residues: 0 loop : -2.95 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 251 TYR 0.020 0.002 TYR F 153 PHE 0.026 0.002 PHE G 195 TRP 0.042 0.003 TRP D 201 HIS 0.004 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00352 (10293) covalent geometry : angle 0.79386 (13931) hydrogen bonds : bond 0.03551 ( 648) hydrogen bonds : angle 4.61498 ( 1917) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 251 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 LYS cc_start: 0.7332 (ttmt) cc_final: 0.6771 (mmtm) REVERT: G 130 THR cc_start: 0.8292 (m) cc_final: 0.8033 (p) REVERT: G 206 ASN cc_start: 0.7337 (OUTLIER) cc_final: 0.6860 (t0) REVERT: F 85 TRP cc_start: 0.7451 (m-10) cc_final: 0.7201 (m-10) REVERT: F 131 GLU cc_start: 0.7622 (mt-10) cc_final: 0.6908 (mp0) REVERT: F 208 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7128 (mm) REVERT: F 241 LYS cc_start: 0.6461 (pttt) cc_final: 0.6094 (pttp) REVERT: E 131 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7477 (pt0) REVERT: E 192 LEU cc_start: 0.7639 (mm) cc_final: 0.7136 (tp) REVERT: E 198 TYR cc_start: 0.6690 (OUTLIER) cc_final: 0.6317 (m-80) REVERT: E 208 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.6883 (mt) REVERT: E 244 MET cc_start: 0.5925 (tpt) cc_final: 0.5603 (tpp) REVERT: D 6 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7244 (tp) REVERT: D 11 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6382 (tt) REVERT: D 20 MET cc_start: 0.7157 (mmm) cc_final: 0.6597 (tpp) outliers start: 44 outliers final: 29 residues processed: 279 average time/residue: 0.0819 time to fit residues: 33.7844 Evaluate side-chains 271 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 206 ASN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 172 HIS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 166 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 76 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 96 optimal weight: 0.0370 chunk 78 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 84 optimal weight: 0.0000 overall best weight: 0.5266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 240 GLN F 120 GLN F 206 ASN E 141 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 HIS ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.176605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.146633 restraints weight = 17727.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.148992 restraints weight = 12053.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.150575 restraints weight = 9438.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.151555 restraints weight = 8134.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.151855 restraints weight = 7438.307| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 10293 Z= 0.146 Angle : 0.822 15.483 13931 Z= 0.404 Chirality : 0.048 0.446 1694 Planarity : 0.004 0.045 1736 Dihedral : 5.090 25.661 1376 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.75 % Allowed : 28.75 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.23), residues: 1310 helix: 0.01 (0.17), residues: 941 sheet: None (None), residues: 0 loop : -2.89 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 251 TYR 0.021 0.002 TYR F 153 PHE 0.032 0.002 PHE D 124 TRP 0.030 0.002 TRP D 201 HIS 0.004 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00327 (10293) covalent geometry : angle 0.82241 (13931) hydrogen bonds : bond 0.03593 ( 648) hydrogen bonds : angle 4.65207 ( 1917) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 261 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 LYS cc_start: 0.7230 (ttmt) cc_final: 0.6709 (mmtm) REVERT: G 130 THR cc_start: 0.8156 (m) cc_final: 0.7879 (p) REVERT: F 131 GLU cc_start: 0.7596 (mt-10) cc_final: 0.6881 (mp0) REVERT: F 208 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.6759 (mt) REVERT: F 241 LYS cc_start: 0.6480 (pttt) cc_final: 0.6111 (pttp) REVERT: E 131 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7475 (pt0) REVERT: E 192 LEU cc_start: 0.7652 (mm) cc_final: 0.7117 (tp) REVERT: E 198 TYR cc_start: 0.6722 (OUTLIER) cc_final: 0.6287 (m-10) REVERT: E 208 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.6821 (mt) REVERT: E 244 MET cc_start: 0.5951 (tpt) cc_final: 0.5647 (tpp) REVERT: D 6 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7195 (tp) REVERT: D 11 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.6262 (tt) REVERT: C 222 MET cc_start: 0.6586 (mtt) cc_final: 0.6379 (mtt) outliers start: 40 outliers final: 29 residues processed: 283 average time/residue: 0.0823 time to fit residues: 34.2548 Evaluate side-chains 278 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 244 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain F residue 172 HIS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 202 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 21 optimal weight: 0.0980 chunk 93 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 240 GLN ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN E 141 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.176323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.145370 restraints weight = 17181.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.147805 restraints weight = 11319.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.149455 restraints weight = 8814.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.150475 restraints weight = 7548.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.150868 restraints weight = 6904.792| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10293 Z= 0.151 Angle : 0.858 18.515 13931 Z= 0.418 Chirality : 0.051 0.740 1694 Planarity : 0.004 0.045 1736 Dihedral : 5.025 25.551 1376 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.84 % Allowed : 29.03 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.23), residues: 1310 helix: 0.05 (0.17), residues: 948 sheet: None (None), residues: 0 loop : -3.03 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 251 TYR 0.027 0.002 TYR F 153 PHE 0.031 0.002 PHE D 124 TRP 0.031 0.003 TRP F 85 HIS 0.004 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00350 (10293) covalent geometry : angle 0.85787 (13931) hydrogen bonds : bond 0.03626 ( 648) hydrogen bonds : angle 4.66452 ( 1917) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 256 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 LYS cc_start: 0.7229 (ttmt) cc_final: 0.6726 (mmtm) REVERT: G 130 THR cc_start: 0.8156 (m) cc_final: 0.7902 (p) REVERT: F 131 GLU cc_start: 0.7590 (mt-10) cc_final: 0.6883 (mp0) REVERT: F 208 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.6589 (mt) REVERT: F 241 LYS cc_start: 0.6432 (pttt) cc_final: 0.6069 (pttp) REVERT: E 131 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7504 (pt0) REVERT: E 192 LEU cc_start: 0.7666 (mm) cc_final: 0.7162 (tp) REVERT: E 198 TYR cc_start: 0.6773 (OUTLIER) cc_final: 0.6234 (m-10) REVERT: E 208 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.6933 (mt) REVERT: E 244 MET cc_start: 0.5879 (tpt) cc_final: 0.5591 (tpp) REVERT: D 6 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7048 (tp) REVERT: D 11 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6267 (tt) REVERT: C 72 GLN cc_start: 0.6687 (pm20) cc_final: 0.6480 (tt0) REVERT: C 222 MET cc_start: 0.6452 (mtt) cc_final: 0.6216 (mtt) outliers start: 41 outliers final: 31 residues processed: 282 average time/residue: 0.0841 time to fit residues: 34.8289 Evaluate side-chains 277 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 241 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 172 HIS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 202 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 77 optimal weight: 0.0470 chunk 31 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 57 optimal weight: 0.0050 chunk 123 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 89 optimal weight: 0.0070 overall best weight: 0.3912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 GLN F 120 GLN F 206 ASN E 141 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 HIS ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.178068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.148310 restraints weight = 17828.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.150690 restraints weight = 12089.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.152275 restraints weight = 9444.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.152998 restraints weight = 8146.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.153254 restraints weight = 7532.992| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 10293 Z= 0.150 Angle : 0.881 19.038 13931 Z= 0.426 Chirality : 0.051 0.700 1694 Planarity : 0.004 0.046 1736 Dihedral : 4.967 25.393 1376 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.46 % Allowed : 29.40 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.23), residues: 1310 helix: 0.10 (0.17), residues: 949 sheet: None (None), residues: 0 loop : -3.01 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 251 TYR 0.037 0.001 TYR F 153 PHE 0.036 0.002 PHE G 187 TRP 0.040 0.003 TRP F 85 HIS 0.004 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00341 (10293) covalent geometry : angle 0.88102 (13931) hydrogen bonds : bond 0.03629 ( 648) hydrogen bonds : angle 4.68506 ( 1917) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1805.66 seconds wall clock time: 31 minutes 44.32 seconds (1904.32 seconds total)