Starting phenix.real_space_refine on Wed Aug 5 21:27:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13hr_77072/08_2026/13hr_77072.cif Found real_map, /net/cci-nas-00/data/ceres_data/13hr_77072/08_2026/13hr_77072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/13hr_77072/08_2026/13hr_77072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13hr_77072/08_2026/13hr_77072.map" model { file = "/net/cci-nas-00/data/ceres_data/13hr_77072/08_2026/13hr_77072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13hr_77072/08_2026/13hr_77072.cif" } resolution = 2.7 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= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 7192 2.51 5 N 2160 2.21 5 O 2160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11520 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1380 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 12, 'TRANS': 165} Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 60 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5} Restraints were copied for chains: B, C, D, E, F, G, H, J, K, L, M, N, O, P Time building chain proxies: 1.70, per 1000 atoms: 0.15 Number of scatterers: 11520 At special positions: 0 Unit cell: (113.715, 113.715, 68.229, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 8 16.00 O 2160 8.00 N 2160 7.00 C 7192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 481.8 milliseconds 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2800 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 1 sheets defined 30.8% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 66 through 71 removed outlier: 3.828A pdb=" N SER A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 111 Processing helix chain 'A' and resid 140 through 144 removed outlier: 3.669A pdb=" N GLY A 143 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 207 removed outlier: 3.991A pdb=" N SER A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 71 removed outlier: 3.828A pdb=" N SER B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 111 Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.669A pdb=" N GLY B 143 " --> pdb=" O TYR B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 207 removed outlier: 3.990A pdb=" N SER B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 removed outlier: 3.828A pdb=" N SER C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 111 Processing helix chain 'C' and resid 140 through 144 removed outlier: 3.669A pdb=" N GLY C 143 " --> pdb=" O TYR C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 207 removed outlier: 3.992A pdb=" N SER C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 71 removed outlier: 3.828A pdb=" N SER D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 111 Processing helix chain 'D' and resid 140 through 144 removed outlier: 3.669A pdb=" N GLY D 143 " --> pdb=" O TYR D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 207 removed outlier: 3.991A pdb=" N SER D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR D 193 " --> pdb=" O LYS D 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 71 removed outlier: 3.828A pdb=" N SER E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 111 Processing helix chain 'E' and resid 140 through 144 removed outlier: 3.669A pdb=" N GLY E 143 " --> pdb=" O TYR E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 207 removed outlier: 3.991A pdb=" N SER E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA E 186 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR E 193 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 71 removed outlier: 3.828A pdb=" N SER F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 111 Processing helix chain 'F' and resid 140 through 144 removed outlier: 3.669A pdb=" N GLY F 143 " --> pdb=" O TYR F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 207 removed outlier: 3.991A pdb=" N SER F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA F 186 " --> pdb=" O ALA F 182 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR F 193 " --> pdb=" O LYS F 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 71 removed outlier: 3.828A pdb=" N SER G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 111 Processing helix chain 'G' and resid 140 through 144 removed outlier: 3.669A pdb=" N GLY G 143 " --> pdb=" O TYR G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 207 removed outlier: 3.991A pdb=" N SER G 185 " --> pdb=" O ALA G 181 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA G 186 " --> pdb=" O ALA G 182 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR G 193 " --> pdb=" O LYS G 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 71 removed outlier: 3.828A pdb=" N SER H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 111 Processing helix chain 'H' and resid 140 through 144 removed outlier: 3.669A pdb=" N GLY H 143 " --> pdb=" O TYR H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 207 removed outlier: 3.991A pdb=" N SER H 185 " --> pdb=" O ALA H 181 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA H 186 " --> pdb=" O ALA H 182 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR H 193 " --> pdb=" O LYS H 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 36 through 38 current: chain 'A' and resid 82 through 91 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 82 through 91 current: chain 'A' and resid 146 through 157 removed outlier: 6.437A pdb=" N ALA A 147 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER A 172 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 149 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU A 170 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR A 151 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG A 168 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA A 153 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER A 166 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 155 " --> pdb=" O VAL A 164 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 162 through 174 current: chain 'B' and resid 82 through 91 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 82 through 91 current: chain 'B' and resid 146 through 157 removed outlier: 6.438A pdb=" N ALA B 147 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER B 172 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B 149 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU B 170 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR B 151 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG B 168 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA B 153 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER B 166 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 155 " --> pdb=" O VAL B 164 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 162 through 174 current: chain 'C' and resid 82 through 91 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 82 through 91 current: chain 'C' and resid 146 through 157 removed outlier: 6.437A pdb=" N ALA C 147 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER C 172 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE C 149 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU C 170 " --> pdb=" O ILE C 149 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR C 151 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG C 168 " --> pdb=" O TYR C 151 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA C 153 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER C 166 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU C 155 " --> pdb=" O VAL C 164 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 162 through 174 current: chain 'D' and resid 82 through 91 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 82 through 91 current: chain 'D' and resid 146 through 157 removed outlier: 6.437A pdb=" N ALA D 147 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER D 172 " --> pdb=" O ALA D 147 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE D 149 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU D 170 " --> pdb=" O ILE D 149 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR D 151 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG D 168 " --> pdb=" O TYR D 151 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA D 153 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER D 166 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU D 155 " --> pdb=" O VAL D 164 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 162 through 174 current: chain 'E' and resid 82 through 91 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 82 through 91 current: chain 'E' and resid 146 through 157 removed outlier: 6.437A pdb=" N ALA E 147 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER E 172 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE E 149 " --> pdb=" O GLU E 170 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU E 170 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR E 151 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG E 168 " --> pdb=" O TYR E 151 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA E 153 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER E 166 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU E 155 " --> pdb=" O VAL E 164 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 162 through 174 current: chain 'F' and resid 82 through 91 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 82 through 91 current: chain 'F' and resid 146 through 157 removed outlier: 6.437A pdb=" N ALA F 147 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER F 172 " --> pdb=" O ALA F 147 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE F 149 " --> pdb=" O GLU F 170 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU F 170 " --> pdb=" O ILE F 149 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR F 151 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG F 168 " --> pdb=" O TYR F 151 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA F 153 " --> pdb=" O SER F 166 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER F 166 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU F 155 " --> pdb=" O VAL F 164 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 162 through 174 current: chain 'G' and resid 82 through 91 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 82 through 91 current: chain 'G' and resid 146 through 157 removed outlier: 6.437A pdb=" N ALA G 147 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER G 172 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE G 149 " --> pdb=" O GLU G 170 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU G 170 " --> pdb=" O ILE G 149 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR G 151 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG G 168 " --> pdb=" O TYR G 151 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA G 153 " --> pdb=" O SER G 166 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER G 166 " --> pdb=" O ALA G 153 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU G 155 " --> pdb=" O VAL G 164 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 162 through 174 current: chain 'H' and resid 82 through 91 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 82 through 91 current: chain 'H' and resid 146 through 157 removed outlier: 6.437A pdb=" N ALA H 147 " --> pdb=" O SER H 172 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER H 172 " --> pdb=" O ALA H 147 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE H 149 " --> pdb=" O GLU H 170 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU H 170 " --> pdb=" O ILE H 149 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR H 151 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG H 168 " --> pdb=" O TYR H 151 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA H 153 " --> pdb=" O SER H 166 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER H 166 " --> pdb=" O ALA H 153 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU H 155 " --> pdb=" O VAL H 164 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4000 1.34 - 1.46: 1609 1.46 - 1.57: 6127 1.57 - 1.68: 0 1.68 - 1.80: 16 Bond restraints: 11752 Sorted by residual: bond pdb=" C ALA D 95 " pdb=" N PRO D 96 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.28e-02 6.10e+03 6.20e-01 bond pdb=" C ALA C 95 " pdb=" N PRO C 96 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.28e-02 6.10e+03 6.14e-01 bond pdb=" C ALA A 95 " pdb=" N PRO A 96 " ideal model delta sigma weight residual 1.335 1.344 -0.010 1.28e-02 6.10e+03 5.94e-01 bond pdb=" C ALA G 95 " pdb=" N PRO G 96 " ideal model delta sigma weight residual 1.335 1.344 -0.010 1.28e-02 6.10e+03 5.77e-01 bond pdb=" C ALA B 95 " pdb=" N PRO B 96 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.36e-02 5.41e+03 4.47e-01 ... (remaining 11747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 15470 1.35 - 2.70: 371 2.70 - 4.05: 71 4.05 - 5.40: 40 5.40 - 6.75: 16 Bond angle restraints: 15968 Sorted by residual: angle pdb=" N PHE A 136 " pdb=" CA PHE A 136 " pdb=" C PHE A 136 " ideal model delta sigma weight residual 110.80 105.95 4.85 2.13e+00 2.20e-01 5.17e+00 angle pdb=" N PHE B 136 " pdb=" CA PHE B 136 " pdb=" C PHE B 136 " ideal model delta sigma weight residual 110.80 105.99 4.81 2.13e+00 2.20e-01 5.11e+00 angle pdb=" N PHE F 136 " pdb=" CA PHE F 136 " pdb=" C PHE F 136 " ideal model delta sigma weight residual 110.80 105.99 4.81 2.13e+00 2.20e-01 5.11e+00 angle pdb=" N PHE H 136 " pdb=" CA PHE H 136 " pdb=" C PHE H 136 " ideal model delta sigma weight residual 110.80 105.99 4.81 2.13e+00 2.20e-01 5.11e+00 angle pdb=" N PHE D 136 " pdb=" CA PHE D 136 " pdb=" C PHE D 136 " ideal model delta sigma weight residual 110.80 105.99 4.81 2.13e+00 2.20e-01 5.11e+00 ... (remaining 15963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.99: 6356 11.99 - 23.97: 620 23.97 - 35.96: 160 35.96 - 47.94: 24 47.94 - 59.93: 64 Dihedral angle restraints: 7224 sinusoidal: 2928 harmonic: 4296 Sorted by residual: dihedral pdb=" CB ARG E 154 " pdb=" CG ARG E 154 " pdb=" CD ARG E 154 " pdb=" NE ARG E 154 " ideal model delta sinusoidal sigma weight residual -180.00 -127.08 -52.92 3 1.50e+01 4.44e-03 9.16e+00 dihedral pdb=" CB ARG G 154 " pdb=" CG ARG G 154 " pdb=" CD ARG G 154 " pdb=" NE ARG G 154 " ideal model delta sinusoidal sigma weight residual -180.00 -127.10 -52.90 3 1.50e+01 4.44e-03 9.16e+00 dihedral pdb=" CB ARG B 154 " pdb=" CG ARG B 154 " pdb=" CD ARG B 154 " pdb=" NE ARG B 154 " ideal model delta sinusoidal sigma weight residual 180.00 -127.11 -52.89 3 1.50e+01 4.44e-03 9.16e+00 ... (remaining 7221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 978 0.026 - 0.053: 457 0.053 - 0.079: 173 0.079 - 0.106: 131 0.106 - 0.132: 29 Chirality restraints: 1768 Sorted by residual: chirality pdb=" CA ILE C 149 " pdb=" N ILE C 149 " pdb=" C ILE C 149 " pdb=" CB ILE C 149 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE D 149 " pdb=" N ILE D 149 " pdb=" C ILE D 149 " pdb=" CB ILE D 149 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE H 149 " pdb=" N ILE H 149 " pdb=" C ILE H 149 " pdb=" CB ILE H 149 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 1765 not shown) Planarity restraints: 2136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 134 " -0.247 9.50e-02 1.11e+02 1.11e-01 1.00e+01 pdb=" NE ARG G 134 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG G 134 " -0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG G 134 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG G 134 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 134 " 0.248 9.50e-02 1.11e+02 1.12e-01 9.99e+00 pdb=" NE ARG C 134 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG C 134 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG C 134 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 134 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 134 " -0.247 9.50e-02 1.11e+02 1.12e-01 9.98e+00 pdb=" NE ARG F 134 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG F 134 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG F 134 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG F 134 " 0.000 2.00e-02 2.50e+03 ... (remaining 2133 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.10: 7481 3.10 - 3.55: 10790 3.55 - 4.00: 17262 4.00 - 4.45: 20710 4.45 - 4.90: 32498 Nonbonded interactions: 88741 Sorted by model distance: nonbonded pdb=" N SER B 84 " pdb=" O SER B 84 " model vdw 2.645 2.496 nonbonded pdb=" N SER F 84 " pdb=" O SER F 84 " model vdw 2.645 2.496 nonbonded pdb=" N SER C 84 " pdb=" O SER C 84 " model vdw 2.645 2.496 nonbonded pdb=" N SER A 84 " pdb=" O SER A 84 " model vdw 2.645 2.496 nonbonded pdb=" N SER E 84 " pdb=" O SER E 84 " model vdw 2.645 2.496 ... (remaining 88736 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.790 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 11752 Z= 0.141 Angle : 0.594 6.751 15968 Z= 0.300 Chirality : 0.043 0.132 1768 Planarity : 0.010 0.112 2136 Dihedral : 11.746 59.927 4424 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.21), residues: 1448 helix: 0.26 (0.26), residues: 392 sheet: 0.06 (0.25), residues: 424 loop : -0.67 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG G 134 TYR 0.005 0.001 TYR A 86 PHE 0.005 0.001 PHE E 169 TRP 0.009 0.001 TRP B 91 HIS 0.001 0.001 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (11752) covalent geometry : angle 0.59372 / 0.30 (15968) hydrogen bonds : bond 0.14264 / 9.81 ( 320) hydrogen bonds : angle 4.72748 / 3.61 ( 912) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.448 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: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.9465 (tp30) cc_final: 0.9027 (tp30) REVERT: A 139 GLU cc_start: 0.9327 (mt-10) cc_final: 0.8745 (mp0) REVERT: J 308 LYS cc_start: 0.8731 (mtpt) cc_final: 0.7729 (mppt) REVERT: K 308 LYS cc_start: 0.8905 (mtpt) cc_final: 0.7870 (mptt) REVERT: K 309 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8369 (tt0) REVERT: L 308 LYS cc_start: 0.8825 (mtpt) cc_final: 0.7856 (mppt) REVERT: M 308 LYS cc_start: 0.8835 (mtpt) cc_final: 0.7831 (mptt) REVERT: M 309 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8846 (mt-10) REVERT: N 308 LYS cc_start: 0.8821 (mtpt) cc_final: 0.7852 (mppt) REVERT: O 308 LYS cc_start: 0.8833 (mtpt) cc_final: 0.7828 (mptt) REVERT: O 309 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8847 (mt-10) REVERT: P 308 LYS cc_start: 0.8814 (mtpt) cc_final: 0.7541 (mptp) REVERT: B 65 THR cc_start: 0.9100 (t) cc_final: 0.8837 (t) REVERT: B 70 GLU cc_start: 0.9484 (tp30) cc_final: 0.8899 (mm-30) REVERT: B 82 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8834 (mt-10) REVERT: B 139 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8648 (mp0) REVERT: C 139 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8573 (mp0) REVERT: C 176 ASP cc_start: 0.9388 (t0) cc_final: 0.9071 (t0) REVERT: D 65 THR cc_start: 0.9131 (t) cc_final: 0.8890 (t) REVERT: D 70 GLU cc_start: 0.9485 (tp30) cc_final: 0.8911 (mm-30) REVERT: D 82 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8704 (mt-10) REVERT: D 139 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8646 (mp0) REVERT: E 67 LEU cc_start: 0.9575 (mt) cc_final: 0.9358 (mm) REVERT: E 70 GLU cc_start: 0.9472 (tp30) cc_final: 0.9016 (tp30) REVERT: E 128 GLU cc_start: 0.9438 (tt0) cc_final: 0.9041 (tm-30) REVERT: E 139 GLU cc_start: 0.9335 (mt-10) cc_final: 0.8770 (mp0) REVERT: F 65 THR cc_start: 0.9133 (t) cc_final: 0.8880 (t) REVERT: F 70 GLU cc_start: 0.9484 (tp30) cc_final: 0.8900 (mm-30) REVERT: F 82 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8669 (mt-10) REVERT: F 139 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8646 (mp0) REVERT: G 67 LEU cc_start: 0.9579 (mt) cc_final: 0.9362 (mm) REVERT: G 70 GLU cc_start: 0.9471 (tp30) cc_final: 0.9014 (tp30) REVERT: G 128 GLU cc_start: 0.9440 (tt0) cc_final: 0.9043 (tm-30) REVERT: G 139 GLU cc_start: 0.9337 (mt-10) cc_final: 0.8769 (mp0) REVERT: H 65 THR cc_start: 0.9100 (t) cc_final: 0.8849 (t) REVERT: H 70 GLU cc_start: 0.9484 (tp30) cc_final: 0.8913 (mm-30) REVERT: H 82 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8744 (mt-10) REVERT: H 139 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8645 (mp0) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.7925 time to fit residues: 161.5824 Evaluate side-chains 116 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0370 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.3980 overall best weight: 2.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.053947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.042208 restraints weight = 38967.953| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 4.48 r_work: 0.2423 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11752 Z= 0.175 Angle : 0.558 5.866 15968 Z= 0.274 Chirality : 0.041 0.126 1768 Planarity : 0.005 0.043 2136 Dihedral : 3.925 35.096 1656 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.49 % Allowed : 10.69 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.21), residues: 1448 helix: 1.32 (0.25), residues: 416 sheet: 0.27 (0.23), residues: 456 loop : -0.86 (0.22), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 62 TYR 0.005 0.001 TYR A 86 PHE 0.013 0.001 PHE I 310 TRP 0.006 0.001 TRP G 201 HIS 0.002 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (11752) covalent geometry : angle 0.55764 / 0.27 (15968) hydrogen bonds : bond 0.05552 / 3.85 ( 320) hydrogen bonds : angle 3.58588 / 2.69 ( 912) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.435 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: symmetry clash REVERT: A 82 GLU cc_start: 0.9321 (mt-10) cc_final: 0.9024 (mt-10) REVERT: A 87 GLN cc_start: 0.8463 (pm20) cc_final: 0.8211 (pm20) REVERT: A 128 GLU cc_start: 0.9411 (tt0) cc_final: 0.8916 (tp30) REVERT: A 139 GLU cc_start: 0.9325 (mt-10) cc_final: 0.8698 (mp0) REVERT: I 308 LYS cc_start: 0.9023 (mtpt) cc_final: 0.7886 (mppt) REVERT: K 308 LYS cc_start: 0.8941 (mtpt) cc_final: 0.7749 (mppt) REVERT: L 308 LYS cc_start: 0.9002 (mtpt) cc_final: 0.7797 (mppt) REVERT: M 308 LYS cc_start: 0.9050 (mtpt) cc_final: 0.7760 (mtmm) REVERT: N 308 LYS cc_start: 0.8976 (mtpt) cc_final: 0.7776 (mppt) REVERT: O 308 LYS cc_start: 0.9032 (mtpt) cc_final: 0.7946 (mptt) REVERT: P 308 LYS cc_start: 0.8937 (mtpt) cc_final: 0.7706 (mppt) REVERT: B 65 THR cc_start: 0.8785 (t) cc_final: 0.7621 (t) REVERT: B 70 GLU cc_start: 0.9428 (tp30) cc_final: 0.8674 (mm-30) REVERT: B 82 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8782 (mt-10) REVERT: B 139 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8838 (mt-10) REVERT: C 70 GLU cc_start: 0.9484 (tp30) cc_final: 0.9070 (tp30) REVERT: C 128 GLU cc_start: 0.9362 (tt0) cc_final: 0.8827 (tp30) REVERT: C 139 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8474 (mp0) REVERT: C 176 ASP cc_start: 0.9414 (t0) cc_final: 0.9158 (t0) REVERT: D 65 THR cc_start: 0.8799 (t) cc_final: 0.7623 (t) REVERT: D 70 GLU cc_start: 0.9421 (tp30) cc_final: 0.8666 (mm-30) REVERT: D 82 GLU cc_start: 0.9261 (mt-10) cc_final: 0.8725 (mt-10) REVERT: D 128 GLU cc_start: 0.9411 (tt0) cc_final: 0.9185 (tt0) REVERT: D 139 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8882 (mt-10) REVERT: E 70 GLU cc_start: 0.9473 (tp30) cc_final: 0.9076 (tp30) REVERT: E 82 GLU cc_start: 0.9320 (mt-10) cc_final: 0.9017 (mt-10) REVERT: E 139 GLU cc_start: 0.9307 (mt-10) cc_final: 0.8691 (mp0) REVERT: F 65 THR cc_start: 0.8825 (t) cc_final: 0.7708 (t) REVERT: F 70 GLU cc_start: 0.9439 (tp30) cc_final: 0.8693 (mm-30) REVERT: F 82 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8684 (mt-10) REVERT: F 128 GLU cc_start: 0.9406 (tt0) cc_final: 0.9179 (tt0) REVERT: F 139 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8880 (mt-10) REVERT: G 70 GLU cc_start: 0.9456 (tp30) cc_final: 0.9054 (tp30) REVERT: G 82 GLU cc_start: 0.9325 (mt-10) cc_final: 0.9019 (mt-10) REVERT: G 139 GLU cc_start: 0.9315 (mt-10) cc_final: 0.8693 (mp0) REVERT: H 65 THR cc_start: 0.8823 (t) cc_final: 0.7678 (t) REVERT: H 70 GLU cc_start: 0.9417 (tp30) cc_final: 0.8660 (mm-30) REVERT: H 82 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8754 (mt-10) REVERT: H 139 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8887 (mt-10) outliers start: 6 outliers final: 0 residues processed: 136 average time/residue: 0.7114 time to fit residues: 102.5091 Evaluate side-chains 115 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 17 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 29 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.050740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.038572 restraints weight = 41082.820| |-----------------------------------------------------------------------------| r_work (start): 0.2475 rms_B_bonded: 4.48 r_work: 0.2288 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 11752 Z= 0.312 Angle : 0.628 6.182 15968 Z= 0.306 Chirality : 0.041 0.115 1768 Planarity : 0.004 0.032 2136 Dihedral : 4.002 27.252 1656 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.82 % Allowed : 11.51 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1448 helix: 2.19 (0.25), residues: 416 sheet: 0.76 (0.27), residues: 304 loop : -0.91 (0.19), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 62 TYR 0.008 0.001 TYR C 86 PHE 0.007 0.001 PHE E 136 TRP 0.006 0.001 TRP E 201 HIS 0.003 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.31 (11752) covalent geometry : angle 0.62760 / 0.31 (15968) hydrogen bonds : bond 0.07345 / 5.12 ( 320) hydrogen bonds : angle 3.72983 / 2.77 ( 912) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.9496 (tp30) cc_final: 0.9021 (tp30) REVERT: A 82 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9142 (mt-10) REVERT: A 128 GLU cc_start: 0.9457 (tt0) cc_final: 0.8936 (tp30) REVERT: A 139 GLU cc_start: 0.9321 (mt-10) cc_final: 0.9025 (mt-10) REVERT: I 308 LYS cc_start: 0.8968 (mtpt) cc_final: 0.7858 (mppt) REVERT: J 308 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.7841 (mppt) REVERT: K 308 LYS cc_start: 0.8848 (mtpt) cc_final: 0.7740 (mppt) REVERT: L 308 LYS cc_start: 0.8944 (mtpt) cc_final: 0.7705 (mptt) REVERT: M 308 LYS cc_start: 0.9006 (mtpt) cc_final: 0.7892 (mppt) REVERT: N 308 LYS cc_start: 0.8926 (mtpt) cc_final: 0.7696 (mptt) REVERT: O 308 LYS cc_start: 0.9012 (mtpt) cc_final: 0.7891 (mppt) REVERT: P 308 LYS cc_start: 0.8915 (mtpt) cc_final: 0.7751 (mppt) REVERT: B 65 THR cc_start: 0.8965 (t) cc_final: 0.8079 (t) REVERT: B 70 GLU cc_start: 0.9442 (tp30) cc_final: 0.8728 (mm-30) REVERT: B 82 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9156 (mt-10) REVERT: B 128 GLU cc_start: 0.9399 (tt0) cc_final: 0.8578 (tp30) REVERT: B 139 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8924 (mt-10) REVERT: C 70 GLU cc_start: 0.9498 (tp30) cc_final: 0.9041 (tp30) REVERT: C 83 ILE cc_start: 0.9575 (tt) cc_final: 0.9356 (tp) REVERT: C 122 ASN cc_start: 0.9192 (t0) cc_final: 0.8988 (t0) REVERT: C 128 GLU cc_start: 0.9455 (tt0) cc_final: 0.8912 (tp30) REVERT: C 139 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8943 (mt-10) REVERT: D 65 THR cc_start: 0.8999 (t) cc_final: 0.8103 (t) REVERT: D 70 GLU cc_start: 0.9446 (tp30) cc_final: 0.8729 (mm-30) REVERT: D 82 GLU cc_start: 0.9411 (mt-10) cc_final: 0.8758 (mt-10) REVERT: D 139 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8935 (mt-10) REVERT: E 70 GLU cc_start: 0.9505 (tp30) cc_final: 0.9031 (tp30) REVERT: E 82 GLU cc_start: 0.9395 (mt-10) cc_final: 0.9092 (mt-10) REVERT: E 122 ASN cc_start: 0.9456 (t0) cc_final: 0.9062 (t0) REVERT: E 128 GLU cc_start: 0.9442 (tt0) cc_final: 0.8884 (tp30) REVERT: E 139 GLU cc_start: 0.9325 (mt-10) cc_final: 0.9036 (mt-10) REVERT: F 65 THR cc_start: 0.8995 (t) cc_final: 0.8114 (t) REVERT: F 70 GLU cc_start: 0.9457 (tp30) cc_final: 0.8749 (mm-30) REVERT: F 82 GLU cc_start: 0.9408 (mt-10) cc_final: 0.8823 (mt-10) REVERT: F 139 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8928 (mt-10) REVERT: G 70 GLU cc_start: 0.9515 (tp30) cc_final: 0.9033 (tp30) REVERT: G 82 GLU cc_start: 0.9440 (mt-10) cc_final: 0.9117 (mt-10) REVERT: G 122 ASN cc_start: 0.9321 (t0) cc_final: 0.9017 (t0) REVERT: G 128 GLU cc_start: 0.9443 (tt0) cc_final: 0.8882 (tp30) REVERT: G 139 GLU cc_start: 0.9323 (mt-10) cc_final: 0.9023 (mt-10) REVERT: G 142 ASN cc_start: 0.9678 (m-40) cc_final: 0.9478 (p0) REVERT: H 65 THR cc_start: 0.9002 (t) cc_final: 0.8128 (t) REVERT: H 70 GLU cc_start: 0.9431 (tp30) cc_final: 0.8723 (mm-30) REVERT: H 82 GLU cc_start: 0.9435 (mt-10) cc_final: 0.8849 (mt-10) REVERT: H 128 GLU cc_start: 0.9391 (tt0) cc_final: 0.8562 (tp30) REVERT: H 139 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8945 (mt-10) outliers start: 10 outliers final: 0 residues processed: 132 average time/residue: 0.7545 time to fit residues: 105.4571 Evaluate side-chains 109 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 308 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 59 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 97 optimal weight: 0.1980 chunk 99 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.051249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.038905 restraints weight = 40114.931| |-----------------------------------------------------------------------------| r_work (start): 0.2510 rms_B_bonded: 4.64 r_work: 0.2320 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11752 Z= 0.146 Angle : 0.518 5.541 15968 Z= 0.247 Chirality : 0.040 0.120 1768 Planarity : 0.004 0.033 2136 Dihedral : 3.805 22.231 1656 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.07 % Allowed : 12.25 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.20), residues: 1448 helix: 2.55 (0.24), residues: 416 sheet: 0.83 (0.27), residues: 304 loop : -0.83 (0.19), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 62 TYR 0.002 0.000 TYR D 151 PHE 0.006 0.001 PHE E 136 TRP 0.004 0.001 TRP H 91 HIS 0.001 0.001 HIS G 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (11752) covalent geometry : angle 0.51785 / 0.25 (15968) hydrogen bonds : bond 0.05781 / 4.01 ( 320) hydrogen bonds : angle 3.35827 / 2.49 ( 912) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.9487 (tp30) cc_final: 0.9054 (tp30) REVERT: A 128 GLU cc_start: 0.9464 (tt0) cc_final: 0.8891 (tp30) REVERT: A 139 GLU cc_start: 0.9358 (mt-10) cc_final: 0.9079 (mt-10) REVERT: I 308 LYS cc_start: 0.8910 (mtpt) cc_final: 0.7775 (mppt) REVERT: K 308 LYS cc_start: 0.8782 (mtpt) cc_final: 0.7762 (mppt) REVERT: L 308 LYS cc_start: 0.8893 (mtpt) cc_final: 0.7776 (mppt) REVERT: M 308 LYS cc_start: 0.8935 (mtpt) cc_final: 0.7756 (mppt) REVERT: M 309 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8469 (tm-30) REVERT: N 308 LYS cc_start: 0.8859 (mtpt) cc_final: 0.7744 (mppt) REVERT: O 308 LYS cc_start: 0.8933 (mtpt) cc_final: 0.7762 (mppt) REVERT: O 309 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8467 (tm-30) REVERT: P 308 LYS cc_start: 0.8864 (mtpt) cc_final: 0.7728 (mppt) REVERT: B 82 GLU cc_start: 0.9401 (mt-10) cc_final: 0.9138 (mt-10) REVERT: B 128 GLU cc_start: 0.9399 (tt0) cc_final: 0.8672 (tp30) REVERT: B 139 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8915 (mt-10) REVERT: B 170 GLU cc_start: 0.9395 (OUTLIER) cc_final: 0.8989 (tp30) REVERT: C 70 GLU cc_start: 0.9461 (tp30) cc_final: 0.9084 (tp30) REVERT: C 122 ASN cc_start: 0.9203 (t0) cc_final: 0.8986 (t0) REVERT: C 128 GLU cc_start: 0.9480 (tt0) cc_final: 0.8914 (tp30) REVERT: C 139 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8915 (mt-10) REVERT: C 170 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.8997 (tp30) REVERT: D 82 GLU cc_start: 0.9400 (mt-10) cc_final: 0.9110 (mt-10) REVERT: D 128 GLU cc_start: 0.9363 (tt0) cc_final: 0.8541 (tp30) REVERT: D 139 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8917 (mt-10) REVERT: D 170 GLU cc_start: 0.9371 (OUTLIER) cc_final: 0.8966 (tp30) REVERT: E 70 GLU cc_start: 0.9483 (tp30) cc_final: 0.9058 (tp30) REVERT: E 122 ASN cc_start: 0.9368 (t0) cc_final: 0.9031 (t0) REVERT: E 128 GLU cc_start: 0.9455 (tt0) cc_final: 0.8926 (tp30) REVERT: E 139 GLU cc_start: 0.9364 (mt-10) cc_final: 0.9085 (mt-10) REVERT: E 170 GLU cc_start: 0.9311 (OUTLIER) cc_final: 0.9018 (tp30) REVERT: F 82 GLU cc_start: 0.9398 (mt-10) cc_final: 0.9113 (mt-10) REVERT: F 128 GLU cc_start: 0.9373 (tt0) cc_final: 0.8559 (tp30) REVERT: F 139 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8921 (mt-10) REVERT: F 170 GLU cc_start: 0.9402 (OUTLIER) cc_final: 0.8997 (tp30) REVERT: G 70 GLU cc_start: 0.9493 (tp30) cc_final: 0.9069 (tp30) REVERT: G 122 ASN cc_start: 0.9268 (t0) cc_final: 0.9017 (t0) REVERT: G 128 GLU cc_start: 0.9459 (tt0) cc_final: 0.8929 (tp30) REVERT: G 139 GLU cc_start: 0.9325 (mt-10) cc_final: 0.8632 (mp0) REVERT: G 142 ASN cc_start: 0.9695 (m-40) cc_final: 0.9494 (p0) REVERT: G 170 GLU cc_start: 0.9314 (OUTLIER) cc_final: 0.9020 (tp30) REVERT: H 82 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9137 (mt-10) REVERT: H 128 GLU cc_start: 0.9398 (tt0) cc_final: 0.8669 (tp30) REVERT: H 139 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8929 (mt-10) REVERT: H 170 GLU cc_start: 0.9380 (OUTLIER) cc_final: 0.8974 (tp30) outliers start: 13 outliers final: 0 residues processed: 132 average time/residue: 0.6861 time to fit residues: 95.9270 Evaluate side-chains 121 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain H residue 170 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 72 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.051134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.038916 restraints weight = 39890.474| |-----------------------------------------------------------------------------| r_work (start): 0.2511 rms_B_bonded: 4.60 r_work: 0.2321 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11752 Z= 0.168 Angle : 0.522 5.754 15968 Z= 0.248 Chirality : 0.039 0.130 1768 Planarity : 0.004 0.033 2136 Dihedral : 3.701 16.658 1656 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.48 % Allowed : 12.58 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.20), residues: 1448 helix: 2.90 (0.24), residues: 416 sheet: 0.88 (0.27), residues: 304 loop : -0.83 (0.19), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 62 TYR 0.003 0.000 TYR C 86 PHE 0.005 0.001 PHE N 310 TRP 0.005 0.001 TRP H 91 HIS 0.002 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (11752) covalent geometry : angle 0.52191 / 0.25 (15968) hydrogen bonds : bond 0.05496 / 3.82 ( 320) hydrogen bonds : angle 3.33211 / 2.48 ( 912) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.9471 (tp30) cc_final: 0.9065 (tp30) REVERT: A 87 GLN cc_start: 0.8392 (pm20) cc_final: 0.8143 (pm20) REVERT: A 128 GLU cc_start: 0.9429 (tt0) cc_final: 0.8856 (tp30) REVERT: A 139 GLU cc_start: 0.9301 (mt-10) cc_final: 0.9045 (mt-10) REVERT: A 170 GLU cc_start: 0.9309 (OUTLIER) cc_final: 0.9029 (tp30) REVERT: I 308 LYS cc_start: 0.8935 (mtpt) cc_final: 0.7790 (mppt) REVERT: K 308 LYS cc_start: 0.8760 (mtpt) cc_final: 0.7789 (tppt) REVERT: L 308 LYS cc_start: 0.8888 (mtpt) cc_final: 0.7738 (mppt) REVERT: M 308 LYS cc_start: 0.8944 (mtpt) cc_final: 0.7874 (mppt) REVERT: N 308 LYS cc_start: 0.8658 (mtpt) cc_final: 0.7446 (mppt) REVERT: O 308 LYS cc_start: 0.8948 (mtpt) cc_final: 0.7897 (mppt) REVERT: P 308 LYS cc_start: 0.8889 (mtpt) cc_final: 0.7716 (mppt) REVERT: B 82 GLU cc_start: 0.9388 (mt-10) cc_final: 0.9135 (mt-10) REVERT: B 128 GLU cc_start: 0.9390 (tt0) cc_final: 0.8721 (tp30) REVERT: B 139 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8904 (mt-10) REVERT: B 170 GLU cc_start: 0.9394 (OUTLIER) cc_final: 0.8986 (tp30) REVERT: B 178 LYS cc_start: 0.9554 (mtpp) cc_final: 0.9170 (mppt) REVERT: C 70 GLU cc_start: 0.9455 (tp30) cc_final: 0.9094 (tp30) REVERT: C 122 ASN cc_start: 0.9182 (t0) cc_final: 0.8929 (t0) REVERT: C 128 GLU cc_start: 0.9472 (tt0) cc_final: 0.8901 (tp30) REVERT: C 139 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8971 (mt-10) REVERT: C 170 GLU cc_start: 0.9291 (OUTLIER) cc_final: 0.8999 (tp30) REVERT: D 82 GLU cc_start: 0.9367 (mt-10) cc_final: 0.9097 (mt-10) REVERT: D 128 GLU cc_start: 0.9385 (tt0) cc_final: 0.8659 (tp30) REVERT: D 139 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8912 (mt-10) REVERT: D 170 GLU cc_start: 0.9367 (OUTLIER) cc_final: 0.8960 (tp30) REVERT: D 178 LYS cc_start: 0.9545 (mtpp) cc_final: 0.9159 (mppt) REVERT: E 70 GLU cc_start: 0.9475 (tp30) cc_final: 0.9063 (tp30) REVERT: E 122 ASN cc_start: 0.9352 (t0) cc_final: 0.9017 (t0) REVERT: E 128 GLU cc_start: 0.9449 (tt0) cc_final: 0.8938 (tp30) REVERT: E 139 GLU cc_start: 0.9331 (mt-10) cc_final: 0.9072 (mt-10) REVERT: E 170 GLU cc_start: 0.9303 (OUTLIER) cc_final: 0.9016 (tp30) REVERT: F 82 GLU cc_start: 0.9363 (mt-10) cc_final: 0.9089 (mt-10) REVERT: F 128 GLU cc_start: 0.9393 (tt0) cc_final: 0.8663 (tp30) REVERT: F 139 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8920 (mt-10) REVERT: F 170 GLU cc_start: 0.9393 (OUTLIER) cc_final: 0.8987 (tp30) REVERT: F 178 LYS cc_start: 0.9581 (mtpp) cc_final: 0.9197 (mppt) REVERT: G 70 GLU cc_start: 0.9488 (tp30) cc_final: 0.9078 (tp30) REVERT: G 122 ASN cc_start: 0.9258 (t0) cc_final: 0.9045 (t0) REVERT: G 128 GLU cc_start: 0.9450 (tt0) cc_final: 0.8937 (tp30) REVERT: G 139 GLU cc_start: 0.9315 (mt-10) cc_final: 0.8612 (mp0) REVERT: G 170 GLU cc_start: 0.9308 (OUTLIER) cc_final: 0.9022 (tp30) REVERT: H 82 GLU cc_start: 0.9389 (mt-10) cc_final: 0.9124 (mt-10) REVERT: H 128 GLU cc_start: 0.9391 (tt0) cc_final: 0.8738 (tp30) REVERT: H 139 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8917 (mt-10) REVERT: H 170 GLU cc_start: 0.9398 (OUTLIER) cc_final: 0.8991 (tp30) REVERT: H 178 LYS cc_start: 0.9556 (mtpp) cc_final: 0.9170 (mppt) outliers start: 18 outliers final: 0 residues processed: 135 average time/residue: 0.7438 time to fit residues: 106.9104 Evaluate side-chains 123 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain H residue 170 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 91 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.050237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.038236 restraints weight = 39960.873| |-----------------------------------------------------------------------------| r_work (start): 0.2499 rms_B_bonded: 4.53 r_work: 0.2314 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 11752 Z= 0.263 Angle : 0.584 6.583 15968 Z= 0.278 Chirality : 0.040 0.157 1768 Planarity : 0.004 0.034 2136 Dihedral : 3.788 15.564 1656 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.07 % Allowed : 13.90 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.21), residues: 1448 helix: 3.10 (0.24), residues: 416 sheet: 0.91 (0.28), residues: 304 loop : -0.90 (0.19), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 52 TYR 0.003 0.001 TYR E 140 PHE 0.006 0.001 PHE F 136 TRP 0.005 0.001 TRP H 91 HIS 0.002 0.001 HIS G 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.26 (11752) covalent geometry : angle 0.58434 / 0.28 (15968) hydrogen bonds : bond 0.06324 / 4.40 ( 320) hydrogen bonds : angle 3.55172 / 2.63 ( 912) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.9499 (tp30) cc_final: 0.9117 (tp30) REVERT: A 128 GLU cc_start: 0.9401 (tt0) cc_final: 0.8873 (tp30) REVERT: A 139 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8576 (mp0) REVERT: A 170 GLU cc_start: 0.9286 (OUTLIER) cc_final: 0.9024 (tp30) REVERT: I 308 LYS cc_start: 0.8934 (mtpt) cc_final: 0.7789 (mppt) REVERT: K 308 LYS cc_start: 0.8778 (mtpt) cc_final: 0.7799 (tppt) REVERT: L 308 LYS cc_start: 0.8928 (mtpt) cc_final: 0.7715 (mppt) REVERT: M 308 LYS cc_start: 0.8861 (mtpt) cc_final: 0.7669 (mppt) REVERT: M 309 GLU cc_start: 0.8620 (tt0) cc_final: 0.8179 (tm-30) REVERT: N 308 LYS cc_start: 0.8646 (mtpt) cc_final: 0.7341 (mppt) REVERT: O 308 LYS cc_start: 0.8885 (mtpt) cc_final: 0.7688 (mppt) REVERT: O 309 GLU cc_start: 0.8647 (tt0) cc_final: 0.8190 (tm-30) REVERT: P 308 LYS cc_start: 0.8926 (mtpt) cc_final: 0.7693 (mppt) REVERT: B 70 GLU cc_start: 0.9435 (tp30) cc_final: 0.9126 (tp30) REVERT: B 82 GLU cc_start: 0.9405 (mt-10) cc_final: 0.8883 (mt-10) REVERT: B 128 GLU cc_start: 0.9390 (tt0) cc_final: 0.8718 (tp30) REVERT: B 139 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8917 (mt-10) REVERT: B 170 GLU cc_start: 0.9349 (OUTLIER) cc_final: 0.9110 (tp30) REVERT: C 70 GLU cc_start: 0.9485 (tp30) cc_final: 0.9038 (tp30) REVERT: C 122 ASN cc_start: 0.9200 (t0) cc_final: 0.8993 (t0) REVERT: C 128 GLU cc_start: 0.9455 (tt0) cc_final: 0.8832 (tp30) REVERT: C 139 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8983 (mt-10) REVERT: C 170 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8935 (tp30) REVERT: D 70 GLU cc_start: 0.9408 (tp30) cc_final: 0.9109 (tp30) REVERT: D 82 GLU cc_start: 0.9388 (mt-10) cc_final: 0.9118 (mt-10) REVERT: D 128 GLU cc_start: 0.9376 (tt0) cc_final: 0.8685 (tp30) REVERT: D 139 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8960 (mt-10) REVERT: D 170 GLU cc_start: 0.9280 (OUTLIER) cc_final: 0.8979 (tp30) REVERT: E 70 GLU cc_start: 0.9486 (tp30) cc_final: 0.9113 (tp30) REVERT: E 122 ASN cc_start: 0.9398 (t0) cc_final: 0.9062 (t0) REVERT: E 128 GLU cc_start: 0.9406 (tt0) cc_final: 0.8869 (tp30) REVERT: E 139 GLU cc_start: 0.9296 (mt-10) cc_final: 0.8616 (mp0) REVERT: E 170 GLU cc_start: 0.9274 (OUTLIER) cc_final: 0.8999 (tp30) REVERT: F 70 GLU cc_start: 0.9437 (tp30) cc_final: 0.9128 (tp30) REVERT: F 82 GLU cc_start: 0.9400 (mt-10) cc_final: 0.8882 (mt-10) REVERT: F 128 GLU cc_start: 0.9376 (tt0) cc_final: 0.8709 (tp30) REVERT: F 139 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8900 (mt-10) REVERT: F 170 GLU cc_start: 0.9358 (OUTLIER) cc_final: 0.9079 (tp30) REVERT: G 70 GLU cc_start: 0.9476 (tp30) cc_final: 0.9076 (tp30) REVERT: G 122 ASN cc_start: 0.9244 (t0) cc_final: 0.8998 (t0) REVERT: G 128 GLU cc_start: 0.9429 (tt0) cc_final: 0.8894 (tp30) REVERT: G 139 GLU cc_start: 0.9299 (mt-10) cc_final: 0.9004 (mt-10) REVERT: G 170 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8936 (tp30) REVERT: H 70 GLU cc_start: 0.9408 (tp30) cc_final: 0.9127 (tp30) REVERT: H 82 GLU cc_start: 0.9404 (mt-10) cc_final: 0.9142 (mt-10) REVERT: H 128 GLU cc_start: 0.9350 (tt0) cc_final: 0.8663 (tp30) REVERT: H 139 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8948 (mt-10) REVERT: H 170 GLU cc_start: 0.9314 (OUTLIER) cc_final: 0.9010 (tp30) outliers start: 13 outliers final: 0 residues processed: 122 average time/residue: 0.8128 time to fit residues: 105.3617 Evaluate side-chains 123 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain H residue 170 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 104 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.050837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.039256 restraints weight = 40891.234| |-----------------------------------------------------------------------------| r_work (start): 0.2510 rms_B_bonded: 4.42 r_work: 0.2328 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11752 Z= 0.207 Angle : 0.575 6.932 15968 Z= 0.270 Chirality : 0.040 0.209 1768 Planarity : 0.004 0.033 2136 Dihedral : 3.805 22.472 1656 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.32 % Allowed : 14.39 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.21), residues: 1448 helix: 3.15 (0.24), residues: 416 sheet: 0.94 (0.28), residues: 304 loop : -0.87 (0.19), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 62 TYR 0.003 0.000 TYR F 86 PHE 0.011 0.001 PHE I 310 TRP 0.005 0.001 TRP H 91 HIS 0.002 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (11752) covalent geometry : angle 0.57469 / 0.27 (15968) hydrogen bonds : bond 0.05834 / 4.07 ( 320) hydrogen bonds : angle 3.43905 / 2.55 ( 912) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.9494 (tp30) cc_final: 0.9106 (tp30) REVERT: A 128 GLU cc_start: 0.9408 (tt0) cc_final: 0.8849 (tp30) REVERT: A 139 GLU cc_start: 0.9265 (mt-10) cc_final: 0.8586 (mp0) REVERT: A 170 GLU cc_start: 0.9343 (OUTLIER) cc_final: 0.9082 (tp30) REVERT: I 308 LYS cc_start: 0.8914 (mtpt) cc_final: 0.7827 (mppt) REVERT: K 308 LYS cc_start: 0.8756 (mtpt) cc_final: 0.7820 (tppt) REVERT: L 308 LYS cc_start: 0.8686 (mtpt) cc_final: 0.7424 (mppt) REVERT: M 308 LYS cc_start: 0.8795 (mtpt) cc_final: 0.7967 (tppt) REVERT: M 309 GLU cc_start: 0.8674 (tt0) cc_final: 0.8274 (tm-30) REVERT: N 308 LYS cc_start: 0.8587 (mtpt) cc_final: 0.7471 (tppt) REVERT: O 308 LYS cc_start: 0.8829 (mtpt) cc_final: 0.7985 (tppt) REVERT: O 309 GLU cc_start: 0.8696 (tt0) cc_final: 0.8280 (tm-30) REVERT: P 308 LYS cc_start: 0.8919 (mtpt) cc_final: 0.7730 (mppt) REVERT: B 70 GLU cc_start: 0.9419 (tp30) cc_final: 0.9049 (tp30) REVERT: B 82 GLU cc_start: 0.9410 (mt-10) cc_final: 0.8908 (mt-10) REVERT: B 128 GLU cc_start: 0.9397 (tt0) cc_final: 0.8746 (tp30) REVERT: B 139 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8928 (mt-10) REVERT: B 170 GLU cc_start: 0.9377 (OUTLIER) cc_final: 0.9037 (tp30) REVERT: B 178 LYS cc_start: 0.9556 (mtpp) cc_final: 0.9189 (mppt) REVERT: C 70 GLU cc_start: 0.9466 (tp30) cc_final: 0.9039 (tp30) REVERT: C 122 ASN cc_start: 0.9212 (t0) cc_final: 0.9011 (t0) REVERT: C 128 GLU cc_start: 0.9452 (tt0) cc_final: 0.8816 (tp30) REVERT: C 139 GLU cc_start: 0.9247 (mt-10) cc_final: 0.9041 (mt-10) REVERT: C 170 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8979 (tp30) REVERT: D 70 GLU cc_start: 0.9383 (tp30) cc_final: 0.9032 (tp30) REVERT: D 82 GLU cc_start: 0.9363 (mt-10) cc_final: 0.8826 (mt-10) REVERT: D 128 GLU cc_start: 0.9376 (tt0) cc_final: 0.8671 (tp30) REVERT: D 139 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8955 (mt-10) REVERT: D 170 GLU cc_start: 0.9296 (OUTLIER) cc_final: 0.8945 (tp30) REVERT: D 178 LYS cc_start: 0.9524 (mtpp) cc_final: 0.9187 (mppt) REVERT: E 70 GLU cc_start: 0.9477 (tp30) cc_final: 0.9103 (tp30) REVERT: E 122 ASN cc_start: 0.9382 (t0) cc_final: 0.9026 (t0) REVERT: E 128 GLU cc_start: 0.9404 (tt0) cc_final: 0.8842 (tp30) REVERT: E 139 GLU cc_start: 0.9292 (mt-10) cc_final: 0.8616 (mp0) REVERT: E 170 GLU cc_start: 0.9318 (OUTLIER) cc_final: 0.9062 (tp30) REVERT: F 70 GLU cc_start: 0.9421 (tp30) cc_final: 0.9053 (tp30) REVERT: F 82 GLU cc_start: 0.9416 (mt-10) cc_final: 0.8916 (mt-10) REVERT: F 128 GLU cc_start: 0.9395 (tt0) cc_final: 0.8717 (tp30) REVERT: F 139 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8901 (mt-10) REVERT: F 170 GLU cc_start: 0.9379 (OUTLIER) cc_final: 0.9043 (tp30) REVERT: F 178 LYS cc_start: 0.9558 (mtpp) cc_final: 0.9204 (mppt) REVERT: G 70 GLU cc_start: 0.9459 (tp30) cc_final: 0.9062 (tp30) REVERT: G 122 ASN cc_start: 0.9254 (t0) cc_final: 0.8996 (t0) REVERT: G 128 GLU cc_start: 0.9428 (tt0) cc_final: 0.8864 (tp30) REVERT: G 139 GLU cc_start: 0.9286 (mt-10) cc_final: 0.9030 (mt-10) REVERT: G 170 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.9011 (tp30) REVERT: H 70 GLU cc_start: 0.9388 (tp30) cc_final: 0.9042 (tp30) REVERT: H 82 GLU cc_start: 0.9395 (mt-10) cc_final: 0.8872 (mt-10) REVERT: H 128 GLU cc_start: 0.9365 (tt0) cc_final: 0.8686 (tp30) REVERT: H 139 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8954 (mt-10) REVERT: H 170 GLU cc_start: 0.9342 (OUTLIER) cc_final: 0.8983 (tp30) REVERT: H 178 LYS cc_start: 0.9533 (mtpp) cc_final: 0.9188 (mppt) outliers start: 16 outliers final: 0 residues processed: 130 average time/residue: 0.7559 time to fit residues: 104.2360 Evaluate side-chains 122 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain H residue 170 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 34 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.050979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.039173 restraints weight = 39195.964| |-----------------------------------------------------------------------------| r_work (start): 0.2525 rms_B_bonded: 4.53 r_work: 0.2342 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11752 Z= 0.169 Angle : 0.554 7.024 15968 Z= 0.262 Chirality : 0.039 0.185 1768 Planarity : 0.003 0.033 2136 Dihedral : 3.785 27.892 1656 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.66 % Allowed : 14.88 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.21), residues: 1448 helix: 3.20 (0.24), residues: 416 sheet: 0.94 (0.28), residues: 304 loop : -0.85 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 62 TYR 0.004 0.000 TYR A 86 PHE 0.008 0.001 PHE I 310 TRP 0.004 0.001 TRP E 91 HIS 0.001 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (11752) covalent geometry : angle 0.55429 / 0.26 (15968) hydrogen bonds : bond 0.05448 / 3.79 ( 320) hydrogen bonds : angle 3.36672 / 2.50 ( 912) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.9495 (tp30) cc_final: 0.9128 (tp30) REVERT: A 128 GLU cc_start: 0.9407 (tt0) cc_final: 0.8840 (tp30) REVERT: A 139 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8981 (mt-10) REVERT: A 170 GLU cc_start: 0.9359 (OUTLIER) cc_final: 0.9106 (tp30) REVERT: I 308 LYS cc_start: 0.8812 (mtpt) cc_final: 0.7620 (mppt) REVERT: I 309 GLU cc_start: 0.8639 (tt0) cc_final: 0.7972 (tm-30) REVERT: K 308 LYS cc_start: 0.8731 (mtpt) cc_final: 0.7781 (tppt) REVERT: L 308 LYS cc_start: 0.8626 (mtpt) cc_final: 0.7469 (tppt) REVERT: M 308 LYS cc_start: 0.8804 (mtpt) cc_final: 0.8014 (tppt) REVERT: N 308 LYS cc_start: 0.8554 (mtpt) cc_final: 0.7281 (mppt) REVERT: O 308 LYS cc_start: 0.8828 (mtpt) cc_final: 0.8035 (tppt) REVERT: P 308 LYS cc_start: 0.8654 (mtpt) cc_final: 0.7351 (mppt) REVERT: B 70 GLU cc_start: 0.9412 (tp30) cc_final: 0.9070 (tp30) REVERT: B 82 GLU cc_start: 0.9406 (mt-10) cc_final: 0.8897 (mt-10) REVERT: B 128 GLU cc_start: 0.9392 (tt0) cc_final: 0.8736 (tp30) REVERT: B 139 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8924 (mt-10) REVERT: B 170 GLU cc_start: 0.9387 (OUTLIER) cc_final: 0.9142 (tp30) REVERT: B 178 LYS cc_start: 0.9551 (mtpp) cc_final: 0.9198 (mppt) REVERT: C 70 GLU cc_start: 0.9460 (tp30) cc_final: 0.9064 (tp30) REVERT: C 122 ASN cc_start: 0.9218 (t0) cc_final: 0.8990 (t0) REVERT: C 128 GLU cc_start: 0.9451 (tt0) cc_final: 0.8803 (tp30) REVERT: C 139 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8609 (mp0) REVERT: C 170 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8989 (tp30) REVERT: D 70 GLU cc_start: 0.9370 (tp30) cc_final: 0.9041 (tp30) REVERT: D 82 GLU cc_start: 0.9359 (mt-10) cc_final: 0.8808 (mt-10) REVERT: D 128 GLU cc_start: 0.9376 (tt0) cc_final: 0.8671 (tp30) REVERT: D 139 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8975 (mt-10) REVERT: D 170 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.9051 (tp30) REVERT: D 178 LYS cc_start: 0.9532 (mtpp) cc_final: 0.9181 (mppt) REVERT: E 70 GLU cc_start: 0.9465 (tp30) cc_final: 0.9123 (tp30) REVERT: E 122 ASN cc_start: 0.9393 (t0) cc_final: 0.9028 (t0) REVERT: E 128 GLU cc_start: 0.9410 (tt0) cc_final: 0.8921 (tp30) REVERT: E 139 GLU cc_start: 0.9265 (mt-10) cc_final: 0.8580 (mp0) REVERT: E 170 GLU cc_start: 0.9318 (OUTLIER) cc_final: 0.9076 (tp30) REVERT: F 70 GLU cc_start: 0.9403 (tp30) cc_final: 0.9053 (tp30) REVERT: F 82 GLU cc_start: 0.9413 (mt-10) cc_final: 0.8908 (mt-10) REVERT: F 128 GLU cc_start: 0.9394 (tt0) cc_final: 0.8725 (tp30) REVERT: F 139 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8920 (mt-10) REVERT: F 170 GLU cc_start: 0.9362 (OUTLIER) cc_final: 0.9130 (tp30) REVERT: F 178 LYS cc_start: 0.9558 (mtpp) cc_final: 0.9172 (mppt) REVERT: G 70 GLU cc_start: 0.9455 (tp30) cc_final: 0.9089 (tp30) REVERT: G 122 ASN cc_start: 0.9260 (t0) cc_final: 0.9004 (t0) REVERT: G 128 GLU cc_start: 0.9424 (tt0) cc_final: 0.8925 (tp30) REVERT: G 139 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8593 (mp0) REVERT: G 170 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.9002 (tp30) REVERT: H 70 GLU cc_start: 0.9372 (tp30) cc_final: 0.9050 (tp30) REVERT: H 82 GLU cc_start: 0.9374 (mt-10) cc_final: 0.8842 (mt-10) REVERT: H 128 GLU cc_start: 0.9356 (tt0) cc_final: 0.8662 (tp30) REVERT: H 139 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8967 (mt-10) REVERT: H 170 GLU cc_start: 0.9336 (OUTLIER) cc_final: 0.9077 (tp30) REVERT: H 178 LYS cc_start: 0.9540 (mtpp) cc_final: 0.9187 (mppt) outliers start: 8 outliers final: 0 residues processed: 119 average time/residue: 0.8073 time to fit residues: 101.5725 Evaluate side-chains 114 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain H residue 170 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 69 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.050045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.038296 restraints weight = 39618.917| |-----------------------------------------------------------------------------| r_work (start): 0.2505 rms_B_bonded: 4.48 r_work: 0.2314 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11752 Z= 0.282 Angle : 0.627 8.333 15968 Z= 0.296 Chirality : 0.041 0.190 1768 Planarity : 0.004 0.034 2136 Dihedral : 3.906 23.785 1656 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.74 % Allowed : 14.72 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.21), residues: 1448 helix: 3.20 (0.25), residues: 416 sheet: 0.91 (0.28), residues: 304 loop : -0.95 (0.19), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 52 TYR 0.003 0.001 TYR D 151 PHE 0.006 0.001 PHE B 136 TRP 0.005 0.001 TRP B 91 HIS 0.003 0.001 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.28 (11752) covalent geometry : angle 0.62712 / 0.30 (15968) hydrogen bonds : bond 0.06371 / 4.44 ( 320) hydrogen bonds : angle 3.62101 / 2.68 ( 912) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.457 Fit side-chains REVERT: A 70 GLU cc_start: 0.9507 (tp30) cc_final: 0.9104 (tp30) REVERT: A 128 GLU cc_start: 0.9415 (tt0) cc_final: 0.8925 (tp30) REVERT: A 139 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8573 (mp0) REVERT: A 170 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.9027 (tp30) REVERT: I 308 LYS cc_start: 0.8816 (mtpt) cc_final: 0.7923 (tppt) REVERT: I 309 GLU cc_start: 0.8653 (tt0) cc_final: 0.7929 (tm-30) REVERT: K 308 LYS cc_start: 0.8729 (mtpt) cc_final: 0.7857 (tppt) REVERT: L 308 LYS cc_start: 0.8560 (mtpt) cc_final: 0.7428 (tppt) REVERT: M 308 LYS cc_start: 0.8658 (mtpt) cc_final: 0.7784 (tppt) REVERT: N 308 LYS cc_start: 0.8522 (mtpt) cc_final: 0.7288 (tppt) REVERT: O 308 LYS cc_start: 0.8669 (mtpt) cc_final: 0.7797 (tppt) REVERT: P 308 LYS cc_start: 0.8659 (mtpt) cc_final: 0.7302 (mppt) REVERT: B 70 GLU cc_start: 0.9397 (tp30) cc_final: 0.9077 (tp30) REVERT: B 82 GLU cc_start: 0.9409 (mt-10) cc_final: 0.8914 (mt-10) REVERT: B 128 GLU cc_start: 0.9407 (tt0) cc_final: 0.8743 (tp30) REVERT: B 139 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8942 (mt-10) REVERT: B 178 LYS cc_start: 0.9552 (mtpp) cc_final: 0.9169 (mppt) REVERT: C 70 GLU cc_start: 0.9480 (tp30) cc_final: 0.9037 (tp30) REVERT: C 122 ASN cc_start: 0.9242 (t0) cc_final: 0.9035 (t0) REVERT: C 128 GLU cc_start: 0.9451 (tt0) cc_final: 0.8821 (tp30) REVERT: C 170 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8953 (tp30) REVERT: D 70 GLU cc_start: 0.9369 (tp30) cc_final: 0.9061 (tp30) REVERT: D 82 GLU cc_start: 0.9382 (mt-10) cc_final: 0.8845 (mt-10) REVERT: D 124 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8894 (tm-30) REVERT: D 128 GLU cc_start: 0.9372 (tt0) cc_final: 0.8688 (tp30) REVERT: D 139 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8983 (mt-10) REVERT: D 170 GLU cc_start: 0.9309 (OUTLIER) cc_final: 0.9103 (tp30) REVERT: D 178 LYS cc_start: 0.9537 (mtpp) cc_final: 0.9158 (mppt) REVERT: E 70 GLU cc_start: 0.9499 (tp30) cc_final: 0.9097 (tp30) REVERT: E 122 ASN cc_start: 0.9392 (t0) cc_final: 0.9037 (t0) REVERT: E 128 GLU cc_start: 0.9419 (tt0) cc_final: 0.8917 (tp30) REVERT: E 139 GLU cc_start: 0.9288 (mt-10) cc_final: 0.8997 (mt-10) REVERT: E 170 GLU cc_start: 0.9297 (OUTLIER) cc_final: 0.9015 (tp30) REVERT: F 70 GLU cc_start: 0.9395 (tp30) cc_final: 0.9069 (tp30) REVERT: F 82 GLU cc_start: 0.9414 (mt-10) cc_final: 0.8904 (mt-10) REVERT: F 128 GLU cc_start: 0.9391 (tt0) cc_final: 0.8735 (tp30) REVERT: F 139 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8928 (mt-10) REVERT: F 178 LYS cc_start: 0.9573 (mtpp) cc_final: 0.9223 (mppt) REVERT: G 70 GLU cc_start: 0.9489 (tp30) cc_final: 0.9057 (tp30) REVERT: G 122 ASN cc_start: 0.9251 (t0) cc_final: 0.8985 (t0) REVERT: G 128 GLU cc_start: 0.9422 (tt0) cc_final: 0.8939 (tp30) REVERT: G 139 GLU cc_start: 0.9306 (mt-10) cc_final: 0.9050 (mt-10) REVERT: G 170 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8961 (tp30) REVERT: H 70 GLU cc_start: 0.9365 (tp30) cc_final: 0.9066 (tp30) REVERT: H 82 GLU cc_start: 0.9430 (mt-10) cc_final: 0.8879 (mt-10) REVERT: H 128 GLU cc_start: 0.9353 (tt0) cc_final: 0.8683 (tp30) REVERT: H 139 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8963 (mt-10) REVERT: H 170 GLU cc_start: 0.9326 (OUTLIER) cc_final: 0.9118 (tp30) REVERT: H 178 LYS cc_start: 0.9555 (mtpp) cc_final: 0.9166 (mppt) outliers start: 9 outliers final: 0 residues processed: 118 average time/residue: 0.8352 time to fit residues: 104.3720 Evaluate side-chains 110 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain H residue 170 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.051627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.039364 restraints weight = 39217.878| |-----------------------------------------------------------------------------| r_work (start): 0.2523 rms_B_bonded: 4.59 r_work: 0.2332 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11752 Z= 0.140 Angle : 0.572 8.107 15968 Z= 0.270 Chirality : 0.040 0.188 1768 Planarity : 0.003 0.033 2136 Dihedral : 3.809 22.593 1656 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.66 % Allowed : 15.05 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.21), residues: 1448 helix: 3.27 (0.25), residues: 416 sheet: 0.94 (0.27), residues: 304 loop : -0.85 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 62 TYR 0.002 0.000 TYR G 151 PHE 0.006 0.001 PHE F 136 TRP 0.004 0.001 TRP C 91 HIS 0.001 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (11752) covalent geometry : angle 0.57249 / 0.27 (15968) hydrogen bonds : bond 0.05166 / 3.59 ( 320) hydrogen bonds : angle 3.30071 / 2.45 ( 912) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.448 Fit side-chains REVERT: A 70 GLU cc_start: 0.9484 (tp30) cc_final: 0.9148 (tp30) REVERT: A 128 GLU cc_start: 0.9434 (tt0) cc_final: 0.8944 (tp30) REVERT: A 139 GLU cc_start: 0.9261 (mt-10) cc_final: 0.8616 (mp0) REVERT: A 170 GLU cc_start: 0.9434 (OUTLIER) cc_final: 0.9170 (tp30) REVERT: A 178 LYS cc_start: 0.9351 (mtpp) cc_final: 0.9100 (mppt) REVERT: I 308 LYS cc_start: 0.8783 (mtpt) cc_final: 0.7913 (tppt) REVERT: I 309 GLU cc_start: 0.8854 (tt0) cc_final: 0.8312 (tm-30) REVERT: J 308 LYS cc_start: 0.8735 (mtpp) cc_final: 0.7751 (ttmt) REVERT: K 308 LYS cc_start: 0.8678 (mtpt) cc_final: 0.7844 (tppt) REVERT: L 308 LYS cc_start: 0.8489 (mtpt) cc_final: 0.7326 (tppt) REVERT: M 308 LYS cc_start: 0.8452 (mtpt) cc_final: 0.7312 (mtmt) REVERT: N 308 LYS cc_start: 0.8444 (mtpt) cc_final: 0.7260 (tppt) REVERT: O 308 LYS cc_start: 0.8464 (mtpt) cc_final: 0.7671 (tppt) REVERT: P 308 LYS cc_start: 0.8591 (mtpt) cc_final: 0.7442 (tppt) REVERT: B 70 GLU cc_start: 0.9364 (tp30) cc_final: 0.9089 (tp30) REVERT: B 82 GLU cc_start: 0.9395 (mt-10) cc_final: 0.8903 (mt-10) REVERT: B 128 GLU cc_start: 0.9390 (tt0) cc_final: 0.8771 (tp30) REVERT: B 139 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8959 (mt-10) REVERT: B 178 LYS cc_start: 0.9555 (mtpp) cc_final: 0.9188 (mppt) REVERT: C 70 GLU cc_start: 0.9493 (tp30) cc_final: 0.9119 (tp30) REVERT: C 122 ASN cc_start: 0.9257 (t0) cc_final: 0.9047 (t0) REVERT: C 128 GLU cc_start: 0.9457 (tt0) cc_final: 0.8809 (tp30) REVERT: C 139 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8505 (mp0) REVERT: C 170 GLU cc_start: 0.9356 (OUTLIER) cc_final: 0.9121 (tp30) REVERT: D 70 GLU cc_start: 0.9331 (tp30) cc_final: 0.9081 (tp30) REVERT: D 82 GLU cc_start: 0.9381 (mt-10) cc_final: 0.8848 (mt-10) REVERT: D 128 GLU cc_start: 0.9366 (tt0) cc_final: 0.8944 (tp30) REVERT: D 139 GLU cc_start: 0.9266 (mt-10) cc_final: 0.9015 (mt-10) REVERT: D 170 GLU cc_start: 0.9389 (OUTLIER) cc_final: 0.9151 (tp30) REVERT: D 178 LYS cc_start: 0.9530 (mtpp) cc_final: 0.9241 (mppt) REVERT: E 70 GLU cc_start: 0.9475 (tp30) cc_final: 0.9147 (tp30) REVERT: E 122 ASN cc_start: 0.9390 (t0) cc_final: 0.9007 (t0) REVERT: E 128 GLU cc_start: 0.9422 (tt0) cc_final: 0.8938 (tp30) REVERT: E 139 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8614 (mp0) REVERT: E 170 GLU cc_start: 0.9386 (OUTLIER) cc_final: 0.9111 (tp30) REVERT: F 70 GLU cc_start: 0.9369 (tp30) cc_final: 0.9095 (tp30) REVERT: F 82 GLU cc_start: 0.9414 (mt-10) cc_final: 0.8900 (mt-10) REVERT: F 128 GLU cc_start: 0.9377 (tt0) cc_final: 0.8974 (tp30) REVERT: F 139 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8957 (mt-10) REVERT: F 178 LYS cc_start: 0.9565 (mtpp) cc_final: 0.9246 (mppt) REVERT: G 70 GLU cc_start: 0.9469 (tp30) cc_final: 0.9115 (tp30) REVERT: G 122 ASN cc_start: 0.9284 (t0) cc_final: 0.9016 (t0) REVERT: G 128 GLU cc_start: 0.9427 (tt0) cc_final: 0.8943 (tp30) REVERT: G 139 GLU cc_start: 0.9292 (mt-10) cc_final: 0.8608 (mp0) REVERT: G 170 GLU cc_start: 0.9363 (OUTLIER) cc_final: 0.9072 (tp30) REVERT: H 70 GLU cc_start: 0.9328 (tp30) cc_final: 0.9085 (tp30) REVERT: H 82 GLU cc_start: 0.9382 (mt-10) cc_final: 0.8860 (mt-10) REVERT: H 128 GLU cc_start: 0.9364 (tt0) cc_final: 0.8733 (tp30) REVERT: H 139 GLU cc_start: 0.9271 (mt-10) cc_final: 0.9019 (mt-10) REVERT: H 170 GLU cc_start: 0.9414 (OUTLIER) cc_final: 0.9170 (tp30) REVERT: H 178 LYS cc_start: 0.9537 (mtpp) cc_final: 0.9233 (mppt) outliers start: 8 outliers final: 0 residues processed: 119 average time/residue: 0.7851 time to fit residues: 98.9808 Evaluate side-chains 120 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain H residue 170 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 106 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.050853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.038685 restraints weight = 39729.528| |-----------------------------------------------------------------------------| r_work (start): 0.2516 rms_B_bonded: 4.58 r_work: 0.2333 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11752 Z= 0.213 Angle : 0.607 8.142 15968 Z= 0.288 Chirality : 0.040 0.188 1768 Planarity : 0.004 0.034 2136 Dihedral : 3.793 20.952 1656 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.49 % Allowed : 15.62 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.21), residues: 1448 helix: 3.34 (0.25), residues: 416 sheet: 0.89 (0.27), residues: 304 loop : -0.87 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 62 TYR 0.003 0.001 TYR B 151 PHE 0.005 0.001 PHE F 136 TRP 0.004 0.001 TRP F 91 HIS 0.002 0.001 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (11752) covalent geometry : angle 0.60665 / 0.29 (15968) hydrogen bonds : bond 0.05722 / 3.98 ( 320) hydrogen bonds : angle 3.45213 / 2.56 ( 912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3105.07 seconds wall clock time: 53 minutes 35.59 seconds (3215.59 seconds total)