Starting phenix.real_space_refine on Mon Aug 25 20:25:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kg0_62304/08_2025/9kg0_62304.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kg0_62304/08_2025/9kg0_62304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kg0_62304/08_2025/9kg0_62304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kg0_62304/08_2025/9kg0_62304.map" model { file = "/net/cci-nas-00/data/ceres_data/9kg0_62304/08_2025/9kg0_62304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kg0_62304/08_2025/9kg0_62304.cif" } resolution = 2.6 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= 0.029 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: 5 Type Number sf(0) Gaussians S 49 5.16 5 C 9947 2.51 5 N 2702 2.21 5 O 3115 1.98 5 H 15037 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30850 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4392 Classifications: {'peptide': 280} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 1 Chain: "B" Number of atoms: 4417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4417 Classifications: {'peptide': 280} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 270} Chain breaks: 1 Chain: "C" Number of atoms: 4417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4417 Classifications: {'peptide': 280} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 1 Chain: "D" Number of atoms: 4395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4395 Classifications: {'peptide': 280} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 1 Chain: "E" Number of atoms: 4417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4417 Classifications: {'peptide': 280} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 270} Chain breaks: 1 Chain: "F" Number of atoms: 4406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4406 Classifications: {'peptide': 280} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 270} Chain breaks: 1 Chain: "G" Number of atoms: 4406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4406 Classifications: {'peptide': 280} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 270} Chain breaks: 1 Time building chain proxies: 6.11, per 1000 atoms: 0.20 Number of scatterers: 30850 At special positions: 0 Unit cell: (112.24, 111.32, 98.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 O 3115 8.00 N 2702 7.00 C 9947 6.00 H 15037 1.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 960.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 25 sheets defined 4.3% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.860A pdb=" N SER A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 6 Processing helix chain 'B' and resid 217 through 223 removed outlier: 4.130A pdb=" N SER B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 removed outlier: 3.845A pdb=" N SER C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 6 removed outlier: 3.669A pdb=" N ILE D 5 " --> pdb=" O ASP D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 223 removed outlier: 4.128A pdb=" N SER D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 removed outlier: 3.530A pdb=" N ILE E 5 " --> pdb=" O ASP E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 222 removed outlier: 4.095A pdb=" N SER E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 6 Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'F' and resid 217 through 223 removed outlier: 4.145A pdb=" N SER F 221 " --> pdb=" O SER F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 6 Processing helix chain 'G' and resid 217 through 223 removed outlier: 4.055A pdb=" N SER G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 29 removed outlier: 3.540A pdb=" N PHE A 39 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA A 229 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR A 101 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 231 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 69 removed outlier: 6.716A pdb=" N GLY A 77 " --> pdb=" O TYR A 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 75 through 89 current: chain 'A' and resid 164 through 171 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 164 through 171 current: chain 'A' and resid 265 through 276 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 265 through 276 current: chain 'A' and resid 290 through 292 Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 113 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 109 through 113 current: chain 'A' and resid 141 through 149 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 141 through 149 current: chain 'B' and resid 140 through 151 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 140 through 151 current: chain 'C' and resid 138 through 149 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 138 through 149 current: chain 'D' and resid 140 through 151 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 140 through 151 current: chain 'E' and resid 140 through 141 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 140 through 141 current: chain 'F' and resid 139 through 149 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 139 through 149 current: chain 'G' and resid 139 through 151 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 22 removed outlier: 3.517A pdb=" N LYS B 51 " --> pdb=" O MET B 234 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET B 234 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA B 229 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR B 101 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 231 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 29 removed outlier: 3.606A pdb=" N ASP B 29 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET B 34 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 75 through 76 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 75 through 76 current: chain 'B' and resid 164 through 171 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 164 through 171 current: chain 'B' and resid 265 through 277 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 265 through 277 current: chain 'B' and resid 290 through 291 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 173 through 176 removed outlier: 3.516A pdb=" N MET B 174 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASN B 176 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLY B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 20 through 22 removed outlier: 3.514A pdb=" N LYS C 21 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL C 231 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 29 removed outlier: 3.819A pdb=" N ASP C 29 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET C 34 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AB2, first strand: chain 'C' and resid 79 through 89 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 79 through 89 current: chain 'C' and resid 165 through 171 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 165 through 171 current: chain 'C' and resid 265 through 270 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 265 through 270 current: chain 'C' and resid 290 through 291 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 21 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 21 through 22 current: chain 'D' and resid 34 through 43 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 51 through 56 current: chain 'D' and resid 229 through 234 Processing sheet with id=AB4, first strand: chain 'D' and resid 70 through 71 removed outlier: 3.633A pdb=" N LYS D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 75 through 76 current: chain 'D' and resid 165 through 171 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 165 through 171 current: chain 'D' and resid 265 through 276 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 265 through 276 current: chain 'D' and resid 290 through 292 Processing sheet with id=AB5, first strand: chain 'D' and resid 174 through 176 removed outlier: 4.709A pdb=" N ASN D 176 " --> pdb=" O GLY D 180 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLY D 180 " --> pdb=" O ASN D 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 20 through 22 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 20 through 22 current: chain 'E' and resid 34 through 43 removed outlier: 3.502A pdb=" N ILE E 43 " --> pdb=" O LEU E 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 52 through 56 current: chain 'E' and resid 229 through 233 Processing sheet with id=AB7, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AB8, first strand: chain 'E' and resid 79 through 89 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 79 through 89 current: chain 'E' and resid 164 through 171 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 164 through 171 current: chain 'E' and resid 275 through 276 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 275 through 276 current: chain 'E' and resid 290 through 292 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 174 through 175 Processing sheet with id=AC1, first strand: chain 'F' and resid 21 through 22 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 40 through 42 current: chain 'F' and resid 229 through 235 Processing sheet with id=AC2, first strand: chain 'F' and resid 26 through 29 removed outlier: 3.584A pdb=" N ASP F 29 " --> pdb=" O MET F 34 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 75 through 76 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 75 through 76 current: chain 'F' and resid 164 through 171 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 164 through 171 current: chain 'F' and resid 265 through 285 Processing sheet with id=AC4, first strand: chain 'F' and resid 174 through 176 removed outlier: 4.778A pdb=" N GLY F 180 " --> pdb=" O ASN F 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 20 through 22 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 20 through 22 current: chain 'G' and resid 34 through 43 removed outlier: 3.599A pdb=" N ILE G 43 " --> pdb=" O LEU G 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 51 through 56 current: chain 'G' and resid 229 through 234 Processing sheet with id=AC6, first strand: chain 'G' and resid 70 through 71 removed outlier: 3.745A pdb=" N LYS G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 75 through 76 current: chain 'G' and resid 164 through 171 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 164 through 171 current: chain 'G' and resid 265 through 279 Processing sheet with id=AC7, first strand: chain 'G' and resid 243 through 244 134 hydrogen bonds defined for protein. 291 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: 7.07 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15037 1.03 - 1.22: 1 1.22 - 1.42: 6974 1.42 - 1.61: 9097 1.61 - 1.80: 98 Bond restraints: 31207 Sorted by residual: bond pdb=" C ASN F 121 " pdb=" N GLY F 122 " ideal model delta sigma weight residual 1.329 1.346 -0.017 1.40e-02 5.10e+03 1.50e+00 bond pdb=" C GLY F 122 " pdb=" O GLY F 122 " ideal model delta sigma weight residual 1.231 1.255 -0.024 2.00e-02 2.50e+03 1.48e+00 bond pdb=" CA GLY A 137 " pdb=" C GLY A 137 " ideal model delta sigma weight residual 1.511 1.524 -0.013 1.08e-02 8.57e+03 1.37e+00 bond pdb=" CA GLY G 137 " pdb=" C GLY G 137 " ideal model delta sigma weight residual 1.512 1.525 -0.013 1.21e-02 6.83e+03 1.12e+00 bond pdb=" CA GLY C 137 " pdb=" C GLY C 137 " ideal model delta sigma weight residual 1.514 1.522 -0.009 8.60e-03 1.35e+04 1.09e+00 ... (remaining 31202 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 53941 1.10 - 2.21: 1979 2.21 - 3.31: 81 3.31 - 4.42: 35 4.42 - 5.52: 1 Bond angle restraints: 56037 Sorted by residual: angle pdb=" N SER F 262 " pdb=" CA SER F 262 " pdb=" CB SER F 262 " ideal model delta sigma weight residual 114.17 110.77 3.40 1.14e+00 7.69e-01 8.88e+00 angle pdb=" N GLY D 137 " pdb=" CA GLY D 137 " pdb=" C GLY D 137 " ideal model delta sigma weight residual 113.18 107.66 5.52 2.37e+00 1.78e-01 5.43e+00 angle pdb=" C ASN D 121 " pdb=" N GLY D 122 " pdb=" CA GLY D 122 " ideal model delta sigma weight residual 121.70 125.34 -3.64 1.80e+00 3.09e-01 4.09e+00 angle pdb=" C PHE D 120 " pdb=" N ASN D 121 " pdb=" CA ASN D 121 " ideal model delta sigma weight residual 122.12 118.66 3.46 1.76e+00 3.23e-01 3.86e+00 angle pdb=" N GLY B 143 " pdb=" CA GLY B 143 " pdb=" C GLY B 143 " ideal model delta sigma weight residual 110.80 113.97 -3.17 1.71e+00 3.42e-01 3.43e+00 ... (remaining 56032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 13986 17.50 - 35.00: 571 35.00 - 52.49: 163 52.49 - 69.99: 53 69.99 - 87.49: 3 Dihedral angle restraints: 14776 sinusoidal: 7902 harmonic: 6874 Sorted by residual: dihedral pdb=" CA ILE F 248 " pdb=" C ILE F 248 " pdb=" N TYR F 249 " pdb=" CA TYR F 249 " ideal model delta harmonic sigma weight residual 180.00 164.22 15.78 0 5.00e+00 4.00e-02 9.96e+00 dihedral pdb=" CA ARG E 253 " pdb=" CB ARG E 253 " pdb=" CG ARG E 253 " pdb=" CD ARG E 253 " ideal model delta sinusoidal sigma weight residual -60.00 -119.10 59.10 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ASP C 100 " pdb=" CA ASP C 100 " pdb=" CB ASP C 100 " pdb=" CG ASP C 100 " ideal model delta sinusoidal sigma weight residual -60.00 -118.13 58.13 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 14773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1348 0.028 - 0.055: 686 0.055 - 0.083: 92 0.083 - 0.111: 128 0.111 - 0.138: 77 Chirality restraints: 2331 Sorted by residual: chirality pdb=" CA ILE D 232 " pdb=" N ILE D 232 " pdb=" C ILE D 232 " pdb=" CB ILE D 232 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA VAL E 140 " pdb=" N VAL E 140 " pdb=" C VAL E 140 " pdb=" CB VAL E 140 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE D 98 " pdb=" N ILE D 98 " pdb=" C ILE D 98 " pdb=" CB ILE D 98 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 2328 not shown) Planarity restraints: 4669 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 138 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" N ASN D 139 " -0.029 2.00e-02 2.50e+03 pdb=" CA ASN D 139 " 0.008 2.00e-02 2.50e+03 pdb=" H ASN D 139 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA E 138 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" N ASN E 139 " -0.024 2.00e-02 2.50e+03 pdb=" CA ASN E 139 " 0.006 2.00e-02 2.50e+03 pdb=" H ASN E 139 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY F 180 " 0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO F 181 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO F 181 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 181 " 0.015 5.00e-02 4.00e+02 ... (remaining 4666 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.00: 302 2.00 - 2.65: 41788 2.65 - 3.30: 87015 3.30 - 3.95: 114762 3.95 - 4.60: 181701 Nonbonded interactions: 425568 Sorted by model distance: nonbonded pdb="HE22 GLN F 242 " pdb=" NZ LYS F 283 " model vdw 1.349 2.080 nonbonded pdb=" HH TYR F 101 " pdb=" OG1 THR G 60 " model vdw 1.583 2.450 nonbonded pdb=" O ASP E 152 " pdb=" H ASN E 172 " model vdw 1.585 2.450 nonbonded pdb=" HH TYR E 101 " pdb=" OG1 THR F 60 " model vdw 1.597 2.450 nonbonded pdb=" HE2 HIS D 48 " pdb=" OD1 ASP E 24 " model vdw 1.603 2.450 ... (remaining 425563 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 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HA )) or resid 31 through 239 or (resid 240 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HA )) or resid 241 through 282 or (resid 283 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name H or \ name HA )) or resid 284 through 293)) selection = (chain 'B' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HA )) or resid 31 through 65 or (resid 66 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or n \ ame NH2 or name H or name HA )) or resid 67 through 74 or (resid 75 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE or na \ me NZ or name H or name HA )) or resid 76 through 239 or (resid 240 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE or na \ me NZ or name H or name HA )) or resid 241 through 261 or (resid 262 and (name N \ or name CA or name C or name O or name CB or name OG or name H or name HA )) or \ resid 263 through 282 or (resid 283 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name CE or name NZ or name H or name HA )) o \ r resid 284 through 293)) selection = (chain 'C' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HA )) or resid 31 through 65 or (resid 66 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or n \ ame NH2 or name H or name HA )) or resid 67 through 74 or (resid 75 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE or na \ me NZ or name H or name HA )) or resid 76 through 239 or (resid 240 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE or na \ me NZ or name H or name HA )) or resid 241 through 261 or (resid 262 and (name N \ or name CA or name C or name O or name CB or name OG or name H or name HA )) or \ resid 263 through 282 or (resid 283 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name CE or name NZ or name H or name HA )) o \ r resid 284 through 293)) selection = (chain 'D' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA )) or resid 67 through 74 or (resid 75 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name CE or \ name NZ or name H or name HA )) or resid 76 through 261 or (resid 262 and (name \ N or name CA or name C or name O or name CB or name OG or name H or name HA )) o \ r resid 263 through 282 or (resid 283 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name CE or name NZ or name H or name HA )) \ or resid 284 through 293)) selection = (chain 'E' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HA )) or resid 31 through 65 or (resid 66 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or n \ ame NH2 or name H or name HA )) or resid 67 through 74 or (resid 75 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE or na \ me NZ or name H or name HA )) or resid 76 through 239 or (resid 240 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE or na \ me NZ or name H or name HA )) or resid 241 through 261 or (resid 262 and (name N \ or name CA or name C or name O or name CB or name OG or name H or name HA )) or \ resid 263 through 282 or (resid 283 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name CE or name NZ or name H or name HA )) o \ r resid 284 through 293)) selection = (chain 'F' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HA )) or resid 31 through 65 or (resid 66 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or n \ ame NH2 or name H or name HA )) or resid 67 through 74 or (resid 75 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE or na \ me NZ or name H or name HA )) or resid 76 through 239 or (resid 240 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE or na \ me NZ or name H or name HA )) or resid 241 through 261 or (resid 262 and (name N \ or name CA or name C or name O or name CB or name OG or name H or name HA )) or \ resid 263 through 293)) selection = (chain 'G' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA )) or resid 67 through 74 or (resid 75 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name CE or \ name NZ or name H or name HA )) or resid 76 through 239 or (resid 240 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name CE or \ name NZ or name H or name HA )) or resid 241 through 261 or (resid 262 and (name \ N or name CA or name C or name O or name CB or name OG or name H or name HA )) \ or resid 263 through 282 or (resid 283 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name CE or name NZ or name H or name HA )) \ or resid 284 through 293)) } 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 individual isotropic 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: 1.550 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: 0.180 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.400 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 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 : 0.004 0.317 16171 Z= 0.286 Angle : 0.468 5.523 21882 Z= 0.258 Chirality : 0.042 0.138 2331 Planarity : 0.002 0.027 2814 Dihedral : 9.674 87.488 5957 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.28 % Favored : 94.62 % Rotamer: Outliers : 0.40 % Allowed : 3.49 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.19), residues: 1932 helix: -0.70 (0.75), residues: 42 sheet: -0.62 (0.17), residues: 1022 loop : -0.90 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 281 TYR 0.010 0.001 TYR A 65 PHE 0.009 0.001 PHE G 153 TRP 0.006 0.001 TRP E 80 HIS 0.003 0.001 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00301 (16170) covalent geometry : angle 0.46838 (21882) hydrogen bonds : bond 0.28037 ( 134) hydrogen bonds : angle 14.12183 ( 291) Misc. bond : bond 0.31692 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 548 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 541 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7739 (m-30) REVERT: A 113 MET cc_start: 0.7893 (ttp) cc_final: 0.7668 (tmm) REVERT: B 94 GLU cc_start: 0.5766 (mm-30) cc_final: 0.5412 (mm-30) REVERT: B 100 ASP cc_start: 0.8156 (m-30) cc_final: 0.7949 (m-30) REVERT: B 139 ASN cc_start: 0.7395 (p0) cc_final: 0.7013 (p0) REVERT: B 185 ASP cc_start: 0.6519 (p0) cc_final: 0.5903 (m-30) REVERT: B 259 HIS cc_start: 0.6826 (p-80) cc_final: 0.6489 (p90) REVERT: C 34 MET cc_start: 0.8017 (ptp) cc_final: 0.7757 (ptp) REVERT: C 87 GLN cc_start: 0.7093 (mt0) cc_final: 0.6846 (mt0) REVERT: C 94 GLU cc_start: 0.5902 (mm-30) cc_final: 0.5650 (mm-30) REVERT: C 100 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7779 (m-30) REVERT: C 179 TRP cc_start: 0.6353 (m100) cc_final: 0.5934 (t-100) REVERT: C 241 GLN cc_start: 0.7161 (mm-40) cc_final: 0.6859 (mm-40) REVERT: C 287 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6526 (tp30) REVERT: D 108 ASP cc_start: 0.6884 (p0) cc_final: 0.6256 (p0) REVERT: D 179 TRP cc_start: 0.6134 (m100) cc_final: 0.5672 (t-100) REVERT: D 198 LYS cc_start: 0.6752 (tptm) cc_final: 0.6400 (ttmt) REVERT: D 205 LYS cc_start: 0.7205 (ttmm) cc_final: 0.6951 (ttpt) REVERT: E 113 MET cc_start: 0.7830 (ttm) cc_final: 0.7495 (ttm) REVERT: E 198 LYS cc_start: 0.6968 (tttp) cc_final: 0.6698 (ttmt) REVERT: E 281 ARG cc_start: 0.7181 (ttm170) cc_final: 0.6960 (ttm-80) REVERT: F 179 TRP cc_start: 0.6380 (t60) cc_final: 0.6064 (t-100) REVERT: F 205 LYS cc_start: 0.7525 (ttmt) cc_final: 0.6999 (ttmt) REVERT: G 75 LYS cc_start: 0.7205 (pttm) cc_final: 0.6887 (ptmt) REVERT: G 152 ASP cc_start: 0.7133 (m-30) cc_final: 0.6833 (m-30) REVERT: G 178 ASN cc_start: 0.7152 (m-40) cc_final: 0.6897 (m-40) REVERT: G 205 LYS cc_start: 0.7361 (ttmm) cc_final: 0.6955 (tttp) outliers start: 7 outliers final: 2 residues processed: 545 average time/residue: 1.4491 time to fit residues: 869.2849 Evaluate side-chains 320 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 316 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain F residue 139 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 49 ASN B 49 ASN B 178 ASN B 241 GLN C 17 ASN C 121 ASN D 32 ASN D 121 ASN D 150 GLN G 87 GLN G 257 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.186811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.174770 restraints weight = 50820.400| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 1.39 r_work: 0.3980 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3862 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16171 Z= 0.099 Angle : 0.478 4.358 21882 Z= 0.253 Chirality : 0.043 0.175 2331 Planarity : 0.003 0.056 2814 Dihedral : 4.089 55.413 2129 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.23 % Favored : 94.67 % Rotamer: Outliers : 2.40 % Allowed : 17.54 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.19), residues: 1932 helix: -0.94 (0.70), residues: 42 sheet: -0.51 (0.17), residues: 1022 loop : -0.88 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 236 TYR 0.011 0.001 TYR F 118 PHE 0.010 0.001 PHE D 42 TRP 0.008 0.001 TRP E 260 HIS 0.005 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00232 (16170) covalent geometry : angle 0.47843 (21882) hydrogen bonds : bond 0.04230 ( 134) hydrogen bonds : angle 9.78870 ( 291) Misc. bond : bond 0.00660 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 390 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 348 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7539 (m-30) REVERT: A 113 MET cc_start: 0.7811 (ttp) cc_final: 0.7605 (tmm) REVERT: B 139 ASN cc_start: 0.7322 (p0) cc_final: 0.6970 (p0) REVERT: B 185 ASP cc_start: 0.6419 (p0) cc_final: 0.5925 (m-30) REVERT: B 240 LYS cc_start: 0.6742 (tttt) cc_final: 0.6374 (tttt) REVERT: B 259 HIS cc_start: 0.6801 (p-80) cc_final: 0.6508 (p90) REVERT: C 34 MET cc_start: 0.7720 (ptp) cc_final: 0.7483 (ptp) REVERT: C 87 GLN cc_start: 0.7281 (mt0) cc_final: 0.7011 (mt0) REVERT: C 100 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7587 (m-30) REVERT: C 179 TRP cc_start: 0.6599 (m100) cc_final: 0.6159 (t-100) REVERT: D 108 ASP cc_start: 0.6513 (p0) cc_final: 0.6050 (p0) REVERT: D 179 TRP cc_start: 0.6190 (m100) cc_final: 0.5661 (t-100) REVERT: D 198 LYS cc_start: 0.6795 (tptm) cc_final: 0.6500 (ttmt) REVERT: D 237 LYS cc_start: 0.8172 (mttt) cc_final: 0.7502 (ptpt) REVERT: D 240 LYS cc_start: 0.6855 (OUTLIER) cc_final: 0.5845 (tptt) REVERT: D 250 GLU cc_start: 0.7139 (tt0) cc_final: 0.6881 (tt0) REVERT: E 100 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7661 (m-30) REVERT: E 198 LYS cc_start: 0.7098 (tttp) cc_final: 0.6886 (ttmt) REVERT: E 242 GLN cc_start: 0.6572 (mp-120) cc_final: 0.6356 (mp10) REVERT: E 287 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6915 (tm-30) REVERT: F 89 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: F 179 TRP cc_start: 0.6664 (t60) cc_final: 0.6382 (t-100) REVERT: F 246 ASP cc_start: 0.7388 (m-30) cc_final: 0.7119 (m-30) REVERT: G 75 LYS cc_start: 0.7190 (pttm) cc_final: 0.6865 (ptmt) REVERT: G 259 HIS cc_start: 0.6636 (p90) cc_final: 0.6285 (p90) outliers start: 42 outliers final: 17 residues processed: 372 average time/residue: 1.1755 time to fit residues: 485.0398 Evaluate side-chains 317 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 294 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 243 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 183 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 180 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 GLN B 242 GLN C 48 HIS C 269 ASN D 121 ASN D 242 GLN E 35 HIS E 242 GLN F 269 ASN G 35 HIS G 105 ASN G 173 ASN G 178 ASN G 201 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.177175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.165001 restraints weight = 50554.701| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 1.34 r_work: 0.3883 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3767 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 16171 Z= 0.298 Angle : 0.677 17.406 21882 Z= 0.362 Chirality : 0.047 0.167 2331 Planarity : 0.005 0.048 2814 Dihedral : 5.156 42.615 2125 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.07 % Favored : 91.87 % Rotamer: Outliers : 6.34 % Allowed : 16.97 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.18), residues: 1932 helix: -3.02 (0.58), residues: 42 sheet: -0.83 (0.16), residues: 1022 loop : -1.43 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 251 TYR 0.019 0.002 TYR F 282 PHE 0.018 0.003 PHE G 153 TRP 0.011 0.002 TRP G 80 HIS 0.015 0.003 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00720 (16170) covalent geometry : angle 0.67659 (21882) hydrogen bonds : bond 0.04932 ( 134) hydrogen bonds : angle 8.65688 ( 291) Misc. bond : bond 0.00542 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 460 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 349 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7655 (m-30) cc_final: 0.7388 (m-30) REVERT: A 108 ASP cc_start: 0.7276 (p0) cc_final: 0.6343 (p0) REVERT: A 174 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7950 (tmm) REVERT: A 175 VAL cc_start: 0.8122 (OUTLIER) cc_final: 0.7787 (p) REVERT: A 235 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.6271 (m-30) REVERT: A 237 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.6953 (pmtt) REVERT: B 139 ASN cc_start: 0.7398 (p0) cc_final: 0.6962 (p0) REVERT: B 152 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.6744 (m-30) REVERT: B 240 LYS cc_start: 0.6949 (tttt) cc_final: 0.6564 (tttt) REVERT: C 34 MET cc_start: 0.7806 (ptp) cc_final: 0.7448 (ptp) REVERT: C 87 GLN cc_start: 0.7638 (mt0) cc_final: 0.7414 (mt0) REVERT: C 94 GLU cc_start: 0.6273 (mm-30) cc_final: 0.6070 (mm-30) REVERT: C 100 ASP cc_start: 0.7954 (m-30) cc_final: 0.7655 (m-30) REVERT: C 179 TRP cc_start: 0.6856 (m100) cc_final: 0.6380 (t-100) REVERT: C 205 LYS cc_start: 0.7577 (mtmm) cc_final: 0.7352 (mtmm) REVERT: C 246 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: C 253 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7422 (mpp80) REVERT: C 292 THR cc_start: 0.7390 (p) cc_final: 0.7031 (m) REVERT: D 31 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6202 (mm-30) REVERT: D 53 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7829 (tp) REVERT: D 108 ASP cc_start: 0.6812 (p0) cc_final: 0.6452 (p0) REVERT: D 179 TRP cc_start: 0.6586 (m100) cc_final: 0.6191 (t-100) REVERT: D 200 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7099 (mpt180) REVERT: D 205 LYS cc_start: 0.7787 (ttpt) cc_final: 0.7041 (tttt) REVERT: D 287 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: E 31 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6033 (mm-30) REVERT: E 100 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7495 (m-30) REVERT: E 198 LYS cc_start: 0.7284 (tttp) cc_final: 0.7038 (ttmt) REVERT: E 234 MET cc_start: 0.7914 (tpp) cc_final: 0.7089 (ttm) REVERT: E 271 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7293 (mtmt) REVERT: E 287 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6945 (tm-30) REVERT: F 205 LYS cc_start: 0.7407 (ttmt) cc_final: 0.6375 (tttt) REVERT: F 208 ASP cc_start: 0.6682 (OUTLIER) cc_final: 0.6406 (p0) REVERT: F 235 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6402 (m-30) REVERT: F 280 GLU cc_start: 0.7504 (tp30) cc_final: 0.7295 (tp30) REVERT: G 31 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6212 (mm-30) REVERT: G 75 LYS cc_start: 0.7266 (pttm) cc_final: 0.6857 (ptmt) REVERT: G 152 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.6736 (m-30) REVERT: G 173 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8139 (p0) REVERT: G 235 ASP cc_start: 0.6978 (OUTLIER) cc_final: 0.6511 (m-30) REVERT: G 253 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.6328 (mtp85) outliers start: 111 outliers final: 37 residues processed: 424 average time/residue: 1.0286 time to fit residues: 488.1224 Evaluate side-chains 356 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 297 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 173 ASN Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 253 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 180 optimal weight: 0.0870 chunk 167 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS B 241 GLN C 150 GLN C 173 ASN C 259 HIS ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN E 214 ASN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN G 150 GLN G 214 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.180765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.168906 restraints weight = 50394.419| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.33 r_work: 0.3927 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3812 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16171 Z= 0.098 Angle : 0.509 8.485 21882 Z= 0.266 Chirality : 0.043 0.155 2331 Planarity : 0.003 0.046 2814 Dihedral : 4.247 34.442 2121 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.12 % Favored : 94.82 % Rotamer: Outliers : 3.03 % Allowed : 21.71 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.18), residues: 1932 helix: -2.91 (0.56), residues: 42 sheet: -0.76 (0.16), residues: 1036 loop : -1.27 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 281 TYR 0.010 0.001 TYR A 65 PHE 0.007 0.001 PHE D 42 TRP 0.008 0.001 TRP A 179 HIS 0.005 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00228 (16170) covalent geometry : angle 0.50890 (21882) hydrogen bonds : bond 0.03147 ( 134) hydrogen bonds : angle 8.07369 ( 291) Misc. bond : bond 0.01195 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 356 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 303 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7479 (m-30) cc_final: 0.7244 (m-30) REVERT: A 174 MET cc_start: 0.8104 (ttp) cc_final: 0.7796 (tmm) REVERT: A 179 TRP cc_start: 0.6729 (t-100) cc_final: 0.6499 (m-90) REVERT: A 220 LEU cc_start: 0.8007 (mt) cc_final: 0.7788 (mm) REVERT: A 234 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7208 (tpt) REVERT: A 235 ASP cc_start: 0.6944 (OUTLIER) cc_final: 0.6431 (m-30) REVERT: B 139 ASN cc_start: 0.7426 (p0) cc_final: 0.6986 (p0) REVERT: B 240 LYS cc_start: 0.6830 (tttt) cc_final: 0.6536 (tttt) REVERT: B 288 LYS cc_start: 0.7384 (mtmt) cc_final: 0.7168 (mtmm) REVERT: C 34 MET cc_start: 0.7735 (ptp) cc_final: 0.7439 (ptp) REVERT: C 87 GLN cc_start: 0.7464 (mt0) cc_final: 0.7249 (mt0) REVERT: C 100 ASP cc_start: 0.7853 (m-30) cc_final: 0.7607 (m-30) REVERT: C 235 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6657 (t70) REVERT: D 108 ASP cc_start: 0.6617 (p0) cc_final: 0.6375 (p0) REVERT: D 183 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7439 (p0) REVERT: D 198 LYS cc_start: 0.7001 (ttmm) cc_final: 0.6795 (ttmt) REVERT: D 200 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7035 (mpt180) REVERT: E 198 LYS cc_start: 0.7185 (tttp) cc_final: 0.6982 (ttmt) REVERT: E 287 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6808 (tm-30) REVERT: F 145 THR cc_start: 0.8273 (p) cc_final: 0.8008 (t) REVERT: G 75 LYS cc_start: 0.7198 (pttm) cc_final: 0.6777 (ptmt) REVERT: G 101 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.6992 (p90) REVERT: G 253 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.6156 (mtp85) outliers start: 53 outliers final: 19 residues processed: 341 average time/residue: 1.2348 time to fit residues: 467.8254 Evaluate side-chains 317 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 290 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 253 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 85 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 42 optimal weight: 0.0870 chunk 93 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 186 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 GLN C 259 HIS ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 214 ASN ** F 194 GLN ** 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 = 0.4092 r_free = 0.4092 target = 0.177355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.165273 restraints weight = 50466.470| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 1.33 r_work: 0.3889 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16171 Z= 0.160 Angle : 0.551 19.245 21882 Z= 0.289 Chirality : 0.043 0.168 2331 Planarity : 0.004 0.041 2814 Dihedral : 4.352 27.201 2121 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.61 % Favored : 92.34 % Rotamer: Outliers : 4.40 % Allowed : 20.74 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.18), residues: 1932 helix: -2.99 (0.43), residues: 77 sheet: -0.86 (0.16), residues: 1036 loop : -1.45 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 66 TYR 0.012 0.001 TYR C 65 PHE 0.010 0.001 PHE A 42 TRP 0.010 0.001 TRP A 260 HIS 0.008 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00381 (16170) covalent geometry : angle 0.55133 (21882) hydrogen bonds : bond 0.03272 ( 134) hydrogen bonds : angle 7.90026 ( 291) Misc. bond : bond 0.00848 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 377 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 300 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7550 (m-30) cc_final: 0.7327 (m-30) REVERT: A 174 MET cc_start: 0.8111 (ttp) cc_final: 0.7907 (tmm) REVERT: A 175 VAL cc_start: 0.8100 (OUTLIER) cc_final: 0.7781 (p) REVERT: A 179 TRP cc_start: 0.6919 (t-100) cc_final: 0.6667 (m-90) REVERT: A 235 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6573 (m-30) REVERT: A 242 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6697 (mt0) REVERT: B 139 ASN cc_start: 0.7541 (p0) cc_final: 0.7082 (p0) REVERT: B 234 MET cc_start: 0.8095 (ttm) cc_final: 0.7245 (ttm) REVERT: B 235 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6576 (m-30) REVERT: B 240 LYS cc_start: 0.6827 (tttt) cc_final: 0.6529 (tttt) REVERT: C 34 MET cc_start: 0.7755 (ptp) cc_final: 0.7456 (ptp) REVERT: C 100 ASP cc_start: 0.7816 (m-30) cc_final: 0.7569 (m-30) REVERT: C 179 TRP cc_start: 0.6853 (m100) cc_final: 0.6426 (t-100) REVERT: C 235 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6673 (t70) REVERT: C 236 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7253 (mtt180) REVERT: C 253 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7220 (mpp80) REVERT: C 292 THR cc_start: 0.6997 (p) cc_final: 0.6579 (m) REVERT: D 183 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7414 (p0) REVERT: D 200 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7113 (mpt180) REVERT: D 287 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7247 (tm-30) REVERT: E 89 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7838 (mt0) REVERT: E 287 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6805 (tm-30) REVERT: G 75 LYS cc_start: 0.7272 (pttm) cc_final: 0.6901 (ptmt) REVERT: G 235 ASP cc_start: 0.6882 (OUTLIER) cc_final: 0.6356 (m-30) REVERT: G 253 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.6235 (mtp85) outliers start: 77 outliers final: 38 residues processed: 346 average time/residue: 1.3077 time to fit residues: 500.9817 Evaluate side-chains 338 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 286 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 236 ARG Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 118 TYR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 253 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 193 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 GLN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN D 121 ASN ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 HIS D 293 ASN E 121 ASN E 177 GLN E 214 ASN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN G 269 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.174703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.162736 restraints weight = 50807.348| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.31 r_work: 0.3864 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 16171 Z= 0.255 Angle : 0.615 6.705 21882 Z= 0.332 Chirality : 0.046 0.161 2331 Planarity : 0.005 0.068 2814 Dihedral : 5.127 39.965 2121 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.97 % Favored : 91.98 % Rotamer: Outliers : 5.71 % Allowed : 20.91 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.28 (0.18), residues: 1932 helix: -3.23 (0.42), residues: 77 sheet: -1.10 (0.15), residues: 1036 loop : -1.71 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 251 TYR 0.016 0.002 TYR C 65 PHE 0.014 0.002 PHE B 84 TRP 0.012 0.002 TRP A 260 HIS 0.009 0.002 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00615 (16170) covalent geometry : angle 0.61541 (21882) hydrogen bonds : bond 0.03857 ( 134) hydrogen bonds : angle 8.06062 ( 291) Misc. bond : bond 0.00699 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 388 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 288 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.6692 (m-30) REVERT: A 174 MET cc_start: 0.8139 (ttp) cc_final: 0.7882 (tmm) REVERT: A 175 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7743 (p) REVERT: A 179 TRP cc_start: 0.7248 (OUTLIER) cc_final: 0.6823 (m-90) REVERT: A 235 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6505 (m-30) REVERT: A 242 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6771 (mt0) REVERT: B 117 THR cc_start: 0.8066 (m) cc_final: 0.7669 (p) REVERT: B 235 ASP cc_start: 0.6981 (OUTLIER) cc_final: 0.6577 (m-30) REVERT: B 250 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7371 (mt-10) REVERT: B 291 MET cc_start: 0.8144 (ttm) cc_final: 0.7889 (ttm) REVERT: C 34 MET cc_start: 0.7811 (ptp) cc_final: 0.7382 (ptp) REVERT: C 100 ASP cc_start: 0.7842 (m-30) cc_final: 0.7608 (m-30) REVERT: C 179 TRP cc_start: 0.6894 (m100) cc_final: 0.6453 (t-100) REVERT: C 235 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6794 (t70) REVERT: C 246 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7726 (m-30) REVERT: C 253 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7297 (mpp80) REVERT: D 183 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7517 (p0) REVERT: D 200 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7133 (mpt180) REVERT: D 205 LYS cc_start: 0.7812 (ttpt) cc_final: 0.7143 (tttt) REVERT: D 240 LYS cc_start: 0.6942 (OUTLIER) cc_final: 0.5977 (tptt) REVERT: D 287 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: E 89 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: E 198 LYS cc_start: 0.7377 (ttmm) cc_final: 0.7061 (ttmt) REVERT: E 287 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6898 (tm-30) REVERT: F 287 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6740 (tm-30) REVERT: G 75 LYS cc_start: 0.7280 (pttm) cc_final: 0.6927 (ptmt) REVERT: G 205 LYS cc_start: 0.7956 (ttpt) cc_final: 0.7206 (tttt) REVERT: G 232 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7402 (pt) REVERT: G 235 ASP cc_start: 0.7028 (OUTLIER) cc_final: 0.6466 (m-30) REVERT: G 253 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.6284 (mtp85) outliers start: 100 outliers final: 43 residues processed: 352 average time/residue: 1.3549 time to fit residues: 526.0114 Evaluate side-chains 333 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 270 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 253 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 177 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN C 173 ASN C 214 ASN ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 214 ASN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.175277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.163361 restraints weight = 50958.279| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 1.32 r_work: 0.3870 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.5755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16171 Z= 0.191 Angle : 0.580 15.381 21882 Z= 0.308 Chirality : 0.044 0.265 2331 Planarity : 0.004 0.060 2814 Dihedral : 5.059 44.447 2121 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.71 % Favored : 92.24 % Rotamer: Outliers : 4.63 % Allowed : 22.63 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.18), residues: 1932 helix: -3.27 (0.41), residues: 77 sheet: -1.15 (0.15), residues: 1036 loop : -1.75 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 281 TYR 0.014 0.002 TYR A 65 PHE 0.010 0.002 PHE G 228 TRP 0.010 0.002 TRP A 260 HIS 0.007 0.002 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00459 (16170) covalent geometry : angle 0.57978 (21882) hydrogen bonds : bond 0.03371 ( 134) hydrogen bonds : angle 7.90255 ( 291) Misc. bond : bond 0.01335 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 354 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 273 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6671 (m-30) REVERT: A 174 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7875 (tmm) REVERT: A 179 TRP cc_start: 0.7130 (OUTLIER) cc_final: 0.6752 (m-90) REVERT: A 235 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6601 (m-30) REVERT: A 242 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6813 (mt0) REVERT: B 117 THR cc_start: 0.8073 (m) cc_final: 0.7674 (p) REVERT: B 152 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6939 (m-30) REVERT: B 191 TYR cc_start: 0.7174 (m-80) cc_final: 0.6944 (m-80) REVERT: B 234 MET cc_start: 0.8039 (ttm) cc_final: 0.7241 (ttm) REVERT: B 235 ASP cc_start: 0.6943 (OUTLIER) cc_final: 0.6510 (m-30) REVERT: C 34 MET cc_start: 0.7838 (ptp) cc_final: 0.7463 (ptp) REVERT: C 100 ASP cc_start: 0.7812 (m-30) cc_final: 0.7566 (m-30) REVERT: C 179 TRP cc_start: 0.6812 (m100) cc_final: 0.6430 (t-100) REVERT: C 235 ASP cc_start: 0.6963 (OUTLIER) cc_final: 0.6647 (t70) REVERT: C 246 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7713 (m-30) REVERT: C 253 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7231 (mpp80) REVERT: C 292 THR cc_start: 0.7257 (p) cc_final: 0.6697 (m) REVERT: D 183 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7546 (p0) REVERT: D 200 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7150 (mpt180) REVERT: D 205 LYS cc_start: 0.7763 (ttpt) cc_final: 0.7064 (tttt) REVERT: D 287 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: E 89 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7823 (mt0) REVERT: E 198 LYS cc_start: 0.7360 (ttmm) cc_final: 0.7011 (ttmt) REVERT: E 287 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6845 (tm-30) REVERT: G 75 LYS cc_start: 0.7258 (pttm) cc_final: 0.6895 (ptmt) REVERT: G 101 TYR cc_start: 0.7677 (OUTLIER) cc_final: 0.7390 (p90) REVERT: G 152 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7154 (m-30) REVERT: G 205 LYS cc_start: 0.7922 (ttpt) cc_final: 0.7191 (tttt) REVERT: G 235 ASP cc_start: 0.6790 (OUTLIER) cc_final: 0.6459 (m-30) REVERT: G 253 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.6215 (mtp85) outliers start: 81 outliers final: 41 residues processed: 329 average time/residue: 1.1428 time to fit residues: 416.7256 Evaluate side-chains 324 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 264 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 118 TYR Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 253 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 69 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 ASN ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 214 ASN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.176663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.164698 restraints weight = 50751.654| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 1.31 r_work: 0.3889 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16171 Z= 0.157 Angle : 0.541 11.368 21882 Z= 0.287 Chirality : 0.043 0.135 2331 Planarity : 0.004 0.050 2814 Dihedral : 4.822 38.490 2121 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.51 % Favored : 92.44 % Rotamer: Outliers : 4.57 % Allowed : 22.80 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.18), residues: 1932 helix: -3.17 (0.43), residues: 77 sheet: -1.14 (0.15), residues: 1036 loop : -1.75 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 104 TYR 0.012 0.001 TYR A 65 PHE 0.009 0.001 PHE A 42 TRP 0.010 0.001 TRP A 260 HIS 0.007 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00376 (16170) covalent geometry : angle 0.54063 (21882) hydrogen bonds : bond 0.03106 ( 134) hydrogen bonds : angle 7.62625 ( 291) Misc. bond : bond 0.00759 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 355 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 275 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.6661 (m-30) REVERT: A 174 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7855 (tmm) REVERT: A 179 TRP cc_start: 0.7235 (OUTLIER) cc_final: 0.6846 (m-90) REVERT: A 235 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6678 (m-30) REVERT: A 287 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7314 (pt0) REVERT: B 117 THR cc_start: 0.8031 (m) cc_final: 0.7618 (p) REVERT: B 191 TYR cc_start: 0.7191 (m-80) cc_final: 0.6948 (m-80) REVERT: B 234 MET cc_start: 0.8061 (ttm) cc_final: 0.7242 (ttm) REVERT: B 235 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6585 (m-30) REVERT: C 34 MET cc_start: 0.7834 (ptp) cc_final: 0.7490 (ptp) REVERT: C 100 ASP cc_start: 0.7783 (m-30) cc_final: 0.7546 (m-30) REVERT: C 179 TRP cc_start: 0.6846 (m100) cc_final: 0.6475 (t-100) REVERT: C 235 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6676 (t70) REVERT: C 246 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: C 253 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7220 (mpp80) REVERT: D 183 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7586 (p0) REVERT: D 200 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7197 (mpt180) REVERT: D 205 LYS cc_start: 0.7641 (ttpt) cc_final: 0.6930 (tttt) REVERT: D 287 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7212 (tm-30) REVERT: E 89 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7804 (mt0) REVERT: E 198 LYS cc_start: 0.7369 (ttmm) cc_final: 0.7039 (ttmt) REVERT: E 287 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6802 (tm-30) REVERT: F 243 THR cc_start: 0.6311 (OUTLIER) cc_final: 0.6097 (t) REVERT: G 75 LYS cc_start: 0.7240 (pttm) cc_final: 0.6867 (ptmt) REVERT: G 101 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.7226 (p90) REVERT: G 205 LYS cc_start: 0.7897 (ttpt) cc_final: 0.7163 (tttt) REVERT: G 235 ASP cc_start: 0.6925 (OUTLIER) cc_final: 0.6577 (m-30) REVERT: G 253 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.6259 (mtp85) outliers start: 80 outliers final: 44 residues processed: 329 average time/residue: 1.1634 time to fit residues: 424.6193 Evaluate side-chains 325 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 264 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 236 ARG Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 118 TYR Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 253 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 131 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN C 214 ASN ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN F 178 ASN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.175681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.163310 restraints weight = 51177.661| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 1.38 r_work: 0.3870 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16171 Z= 0.230 Angle : 0.603 13.557 21882 Z= 0.322 Chirality : 0.045 0.146 2331 Planarity : 0.005 0.057 2814 Dihedral : 5.169 43.114 2121 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.90 % Favored : 91.05 % Rotamer: Outliers : 4.86 % Allowed : 22.86 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.18), residues: 1932 helix: -3.26 (0.43), residues: 77 sheet: -1.26 (0.16), residues: 1029 loop : -1.89 (0.19), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 251 TYR 0.014 0.002 TYR A 65 PHE 0.012 0.002 PHE B 84 TRP 0.013 0.002 TRP A 260 HIS 0.008 0.002 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00553 (16170) covalent geometry : angle 0.60294 (21882) hydrogen bonds : bond 0.03562 ( 134) hydrogen bonds : angle 7.85362 ( 291) Misc. bond : bond 0.01157 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 350 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 265 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.6733 (m-30) REVERT: A 174 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7910 (tmm) REVERT: A 179 TRP cc_start: 0.7254 (OUTLIER) cc_final: 0.6863 (m-90) REVERT: A 190 VAL cc_start: 0.7532 (OUTLIER) cc_final: 0.7327 (p) REVERT: A 235 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6759 (m-30) REVERT: A 242 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6745 (mt0) REVERT: B 117 THR cc_start: 0.8031 (m) cc_final: 0.7522 (p) REVERT: B 152 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.6994 (m-30) REVERT: B 235 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6685 (m-30) REVERT: B 243 THR cc_start: 0.7360 (p) cc_final: 0.7096 (t) REVERT: B 250 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: C 34 MET cc_start: 0.7868 (ptp) cc_final: 0.7519 (ptp) REVERT: C 100 ASP cc_start: 0.7828 (m-30) cc_final: 0.7592 (m-30) REVERT: C 179 TRP cc_start: 0.6983 (m100) cc_final: 0.6665 (t-100) REVERT: C 235 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6662 (t70) REVERT: C 246 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: C 253 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7332 (mpp80) REVERT: C 292 THR cc_start: 0.7274 (p) cc_final: 0.6712 (m) REVERT: D 183 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7612 (p0) REVERT: D 200 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7124 (mpt180) REVERT: D 205 LYS cc_start: 0.7680 (ttpt) cc_final: 0.6954 (tttt) REVERT: D 287 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: E 14 ILE cc_start: 0.5532 (OUTLIER) cc_final: 0.5161 (tt) REVERT: E 89 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7883 (mt0) REVERT: E 198 LYS cc_start: 0.7425 (ttmm) cc_final: 0.7073 (ttmt) REVERT: E 287 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6847 (tm-30) REVERT: F 232 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7626 (pt) REVERT: G 31 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6369 (mm-30) REVERT: G 75 LYS cc_start: 0.7275 (pttm) cc_final: 0.6876 (ptmt) REVERT: G 101 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.7358 (p90) REVERT: G 205 LYS cc_start: 0.7933 (ttpt) cc_final: 0.7184 (tttt) REVERT: G 235 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6750 (m-30) REVERT: G 253 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.6322 (mtp85) outliers start: 85 outliers final: 49 residues processed: 324 average time/residue: 1.2448 time to fit residues: 447.4283 Evaluate side-chains 332 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 260 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 236 ARG Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 118 TYR Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 253 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 50 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 191 optimal weight: 0.7980 chunk 178 optimal weight: 5.9990 chunk 185 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 241 GLN B 293 ASN ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN E 241 GLN F 178 ASN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.178014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.165736 restraints weight = 50727.061| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.39 r_work: 0.3897 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.6001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16171 Z= 0.111 Angle : 0.515 12.266 21882 Z= 0.271 Chirality : 0.043 0.138 2331 Planarity : 0.004 0.055 2814 Dihedral : 4.631 37.947 2121 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.52 % Favored : 93.43 % Rotamer: Outliers : 3.77 % Allowed : 24.06 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.18), residues: 1932 helix: -3.19 (0.43), residues: 77 sheet: -1.07 (0.16), residues: 1008 loop : -1.80 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 281 TYR 0.010 0.001 TYR D 68 PHE 0.010 0.001 PHE C 42 TRP 0.010 0.001 TRP A 260 HIS 0.005 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00260 (16170) covalent geometry : angle 0.51531 (21882) hydrogen bonds : bond 0.02751 ( 134) hydrogen bonds : angle 7.46213 ( 291) Misc. bond : bond 0.00802 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 334 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 268 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.6677 (m-30) REVERT: A 174 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7871 (tmm) REVERT: A 179 TRP cc_start: 0.7133 (OUTLIER) cc_final: 0.6916 (m-90) REVERT: A 235 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6773 (m-30) REVERT: A 242 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6641 (mt0) REVERT: B 117 THR cc_start: 0.8015 (m) cc_final: 0.7488 (p) REVERT: B 152 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.6984 (m-30) REVERT: B 234 MET cc_start: 0.8055 (ttm) cc_final: 0.7215 (ttm) REVERT: C 34 MET cc_start: 0.7870 (ptp) cc_final: 0.7580 (ptp) REVERT: C 100 ASP cc_start: 0.7820 (m-30) cc_final: 0.7601 (m-30) REVERT: C 179 TRP cc_start: 0.7020 (m100) cc_final: 0.6708 (t-100) REVERT: C 235 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6701 (t70) REVERT: C 253 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7224 (mpp80) REVERT: D 183 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7620 (p0) REVERT: D 200 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7149 (mpt180) REVERT: D 205 LYS cc_start: 0.7644 (ttpt) cc_final: 0.6875 (tttt) REVERT: D 287 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: E 53 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7908 (tp) REVERT: E 89 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7779 (mt0) REVERT: E 198 LYS cc_start: 0.7308 (ttmm) cc_final: 0.6997 (ttmt) REVERT: E 234 MET cc_start: 0.8184 (ttm) cc_final: 0.7291 (ttm) REVERT: E 287 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6749 (tm-30) REVERT: G 31 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6422 (mm-30) REVERT: G 75 LYS cc_start: 0.7190 (pttm) cc_final: 0.6798 (ptmt) REVERT: G 101 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.7282 (p90) REVERT: G 205 LYS cc_start: 0.7865 (ttpt) cc_final: 0.7139 (tttt) REVERT: G 235 ASP cc_start: 0.7140 (OUTLIER) cc_final: 0.6771 (m-30) REVERT: G 253 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.6235 (mtp85) outliers start: 66 outliers final: 36 residues processed: 311 average time/residue: 1.2757 time to fit residues: 439.1707 Evaluate side-chains 316 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 262 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 118 TYR Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 253 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 111 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 192 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN C 173 ASN C 214 ASN D 64 GLN ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN E 241 GLN F 178 ASN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.175609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.163690 restraints weight = 51016.908| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 1.32 r_work: 0.3880 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 16171 Z= 0.214 Angle : 0.582 13.276 21882 Z= 0.310 Chirality : 0.044 0.134 2331 Planarity : 0.005 0.057 2814 Dihedral : 4.999 43.304 2121 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.16 % Favored : 90.79 % Rotamer: Outliers : 4.23 % Allowed : 23.89 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.18), residues: 1932 helix: -3.24 (0.43), residues: 77 sheet: -1.16 (0.16), residues: 1008 loop : -1.93 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 281 TYR 0.014 0.002 TYR A 65 PHE 0.012 0.002 PHE C 42 TRP 0.012 0.002 TRP A 260 HIS 0.007 0.002 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00517 (16170) covalent geometry : angle 0.58191 (21882) hydrogen bonds : bond 0.03373 ( 134) hydrogen bonds : angle 7.63140 ( 291) Misc. bond : bond 0.00941 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10857.61 seconds wall clock time: 184 minutes 28.21 seconds (11068.21 seconds total)