Starting phenix.real_space_refine on Thu Mar 5 00:26:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m99_23720/03_2026/7m99_23720.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m99_23720/03_2026/7m99_23720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m99_23720/03_2026/7m99_23720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m99_23720/03_2026/7m99_23720.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m99_23720/03_2026/7m99_23720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m99_23720/03_2026/7m99_23720.map" } resolution = 3.2 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= 0.005 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: 6 Type Number sf(0) Gaussians P 63 5.49 5 Mg 7 5.21 5 S 71 5.16 5 C 10938 2.51 5 N 3198 2.21 5 O 3336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17613 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "F" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "H" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "I" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 420 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "J" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 441 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.14, per 1000 atoms: 0.24 Number of scatterers: 17613 At special positions: 0 Unit cell: (142.31, 133, 119.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 71 16.00 P 63 15.00 Mg 7 11.99 O 3336 8.00 N 3198 7.00 C 10938 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 689.9 milliseconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3856 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 16 sheets defined 60.3% alpha, 4.9% beta 13 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 36 through 53 Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 101 through 113 removed outlier: 3.858A pdb=" N PHE A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 134 removed outlier: 4.658A pdb=" N ASP A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 164 Processing helix chain 'A' and resid 174 through 181 removed outlier: 4.120A pdb=" N ALA A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 190 removed outlier: 3.609A pdb=" N ARG A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.522A pdb=" N LYS A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 238 removed outlier: 4.483A pdb=" N ILE A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 257 Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'B' and resid 20 through 29 Processing helix chain 'B' and resid 36 through 53 Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 101 through 113 removed outlier: 3.858A pdb=" N PHE B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 134 removed outlier: 4.007A pdb=" N ASP B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG B 128 " --> pdb=" O ASP B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 153 through 164 Processing helix chain 'B' and resid 175 through 181 Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 201 through 216 removed outlier: 3.522A pdb=" N LYS B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 238 removed outlier: 4.483A pdb=" N ILE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 257 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'C' and resid 20 through 29 Processing helix chain 'C' and resid 36 through 53 Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 101 through 113 removed outlier: 3.856A pdb=" N PHE C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 134 removed outlier: 3.598A pdb=" N ASP C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'C' and resid 174 through 181 removed outlier: 4.126A pdb=" N ALA C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 removed outlier: 3.511A pdb=" N ARG C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 removed outlier: 3.522A pdb=" N LYS C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 238 removed outlier: 4.345A pdb=" N ILE C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 257 Processing helix chain 'C' and resid 264 through 273 Processing helix chain 'D' and resid 20 through 29 Processing helix chain 'D' and resid 36 through 53 Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.857A pdb=" N PHE D 106 " --> pdb=" O PRO D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 134 Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 174 through 181 removed outlier: 4.110A pdb=" N ALA D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 190 removed outlier: 3.510A pdb=" N ARG D 189 " --> pdb=" O GLN D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 215 removed outlier: 3.522A pdb=" N LYS D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 238 removed outlier: 4.484A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 257 Processing helix chain 'D' and resid 264 through 273 Processing helix chain 'E' and resid 20 through 29 Processing helix chain 'E' and resid 36 through 53 Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 101 through 113 removed outlier: 3.857A pdb=" N PHE E 106 " --> pdb=" O PRO E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 134 removed outlier: 4.658A pdb=" N ASP E 127 " --> pdb=" O SER E 123 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG E 128 " --> pdb=" O ASP E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 174 through 181 removed outlier: 4.081A pdb=" N ALA E 178 " --> pdb=" O ASP E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 190 Processing helix chain 'E' and resid 201 through 215 removed outlier: 3.522A pdb=" N LYS E 205 " --> pdb=" O GLY E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 238 removed outlier: 4.488A pdb=" N ILE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 257 Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'F' and resid 20 through 29 Processing helix chain 'F' and resid 36 through 53 Processing helix chain 'F' and resid 65 through 77 Processing helix chain 'F' and resid 101 through 113 removed outlier: 3.857A pdb=" N PHE F 106 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 134 removed outlier: 3.599A pdb=" N ASP F 127 " --> pdb=" O SER F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 152 No H-bonds generated for 'chain 'F' and resid 150 through 152' Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 174 through 181 removed outlier: 4.110A pdb=" N ALA F 178 " --> pdb=" O ASP F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 190 removed outlier: 3.601A pdb=" N ARG F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 215 removed outlier: 3.522A pdb=" N LYS F 205 " --> pdb=" O GLY F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 238 removed outlier: 4.487A pdb=" N ILE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 257 Processing helix chain 'F' and resid 264 through 273 Processing helix chain 'G' and resid 20 through 29 Processing helix chain 'G' and resid 36 through 53 removed outlier: 3.817A pdb=" N GLY G 48 " --> pdb=" O ASP G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 101 through 113 removed outlier: 3.857A pdb=" N PHE G 106 " --> pdb=" O PRO G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 134 removed outlier: 4.657A pdb=" N ASP G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG G 128 " --> pdb=" O ASP G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 153 through 164 Processing helix chain 'G' and resid 174 through 181 removed outlier: 4.091A pdb=" N ALA G 178 " --> pdb=" O ASP G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 190 removed outlier: 3.533A pdb=" N ARG G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 215 removed outlier: 3.522A pdb=" N LYS G 205 " --> pdb=" O GLY G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 238 removed outlier: 4.489A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 257 Processing helix chain 'G' and resid 264 through 273 Processing helix chain 'H' and resid 20 through 29 Processing helix chain 'H' and resid 36 through 53 Processing helix chain 'H' and resid 65 through 77 Processing helix chain 'H' and resid 101 through 113 removed outlier: 3.857A pdb=" N PHE H 106 " --> pdb=" O PRO H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 134 removed outlier: 4.657A pdb=" N ASP H 127 " --> pdb=" O SER H 123 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG H 128 " --> pdb=" O ASP H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 152 No H-bonds generated for 'chain 'H' and resid 150 through 152' Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 174 through 181 removed outlier: 4.118A pdb=" N ALA H 178 " --> pdb=" O ASP H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 removed outlier: 3.527A pdb=" N ARG H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 215 removed outlier: 3.521A pdb=" N LYS H 205 " --> pdb=" O GLY H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 238 removed outlier: 4.482A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 257 Processing helix chain 'H' and resid 264 through 273 Processing sheet with id=AA1, first strand: chain 'A' and resid 171 through 173 removed outlier: 5.842A pdb=" N VAL A 58 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 94 removed outlier: 6.650A pdb=" N VAL A 92 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 173 removed outlier: 5.905A pdb=" N VAL B 58 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 94 removed outlier: 6.651A pdb=" N VAL B 92 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 171 through 172 removed outlier: 5.858A pdb=" N VAL C 58 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG C 57 " --> pdb=" O LEU C 194 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.651A pdb=" N VAL C 92 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 171 through 172 removed outlier: 5.963A pdb=" N VAL D 58 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 91 through 94 removed outlier: 7.051A pdb=" N VAL D 92 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 171 through 172 removed outlier: 6.002A pdb=" N VAL E 58 " --> pdb=" O GLY E 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.650A pdb=" N VAL E 92 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 171 through 172 removed outlier: 6.283A pdb=" N VAL F 58 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 91 through 94 removed outlier: 6.650A pdb=" N VAL F 92 " --> pdb=" O ILE F 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 171 through 172 removed outlier: 6.124A pdb=" N VAL G 58 " --> pdb=" O GLY G 172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 91 through 94 removed outlier: 6.651A pdb=" N VAL G 92 " --> pdb=" O ILE G 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 171 through 172 removed outlier: 5.963A pdb=" N VAL H 58 " --> pdb=" O GLY H 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 91 through 94 removed outlier: 6.637A pdb=" N VAL H 92 " --> pdb=" O ILE H 142 " (cutoff:3.500A) 802 hydrogen bonds defined for protein. 2406 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.36: 5819 1.36 - 1.54: 11815 1.54 - 1.72: 234 1.72 - 1.90: 96 1.90 - 2.07: 7 Bond restraints: 17971 Sorted by residual: bond pdb=" C4 AGS G 300 " pdb=" C5 AGS G 300 " ideal model delta sigma weight residual 1.386 1.470 -0.084 1.00e-02 1.00e+04 7.03e+01 bond pdb=" C4 AGS H 300 " pdb=" C5 AGS H 300 " ideal model delta sigma weight residual 1.386 1.470 -0.084 1.00e-02 1.00e+04 6.99e+01 bond pdb=" C4 AGS B 300 " pdb=" C5 AGS B 300 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C4 AGS C 300 " pdb=" C5 AGS C 300 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C4 AGS D 300 " pdb=" C5 AGS D 300 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.87e+01 ... (remaining 17966 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 20235 2.11 - 4.22: 3805 4.22 - 6.33: 258 6.33 - 8.44: 65 8.44 - 10.55: 20 Bond angle restraints: 24383 Sorted by residual: angle pdb=" C5 AGS C 300 " pdb=" C4 AGS C 300 " pdb=" N3 AGS C 300 " ideal model delta sigma weight residual 126.80 118.53 8.27 7.41e-01 1.82e+00 1.25e+02 angle pdb=" C5 AGS E 300 " pdb=" C4 AGS E 300 " pdb=" N3 AGS E 300 " ideal model delta sigma weight residual 126.80 118.61 8.19 7.41e-01 1.82e+00 1.22e+02 angle pdb=" C5 AGS G 300 " pdb=" C4 AGS G 300 " pdb=" N3 AGS G 300 " ideal model delta sigma weight residual 126.80 118.62 8.18 7.41e-01 1.82e+00 1.22e+02 angle pdb=" C5 AGS B 300 " pdb=" C4 AGS B 300 " pdb=" N3 AGS B 300 " ideal model delta sigma weight residual 126.80 118.63 8.17 7.41e-01 1.82e+00 1.22e+02 angle pdb=" C5 AGS D 300 " pdb=" C4 AGS D 300 " pdb=" N3 AGS D 300 " ideal model delta sigma weight residual 126.80 118.69 8.11 7.41e-01 1.82e+00 1.20e+02 ... (remaining 24378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 10685 35.96 - 71.92: 379 71.92 - 107.87: 31 107.87 - 143.83: 5 143.83 - 179.79: 10 Dihedral angle restraints: 11110 sinusoidal: 5150 harmonic: 5960 Sorted by residual: dihedral pdb=" O1B AGS E 300 " pdb=" O3B AGS E 300 " pdb=" PB AGS E 300 " pdb=" PG AGS E 300 " ideal model delta sinusoidal sigma weight residual 68.91 -110.88 179.79 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B AGS C 300 " pdb=" O3B AGS C 300 " pdb=" PB AGS C 300 " pdb=" PG AGS C 300 " ideal model delta sinusoidal sigma weight residual 68.91 -119.96 -171.13 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O1A AGS F 300 " pdb=" O3A AGS F 300 " pdb=" PA AGS F 300 " pdb=" PB AGS F 300 " ideal model delta sinusoidal sigma weight residual -67.73 94.94 -162.67 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 11107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1354 0.078 - 0.156: 1094 0.156 - 0.234: 268 0.234 - 0.312: 28 0.312 - 0.390: 10 Chirality restraints: 2754 Sorted by residual: chirality pdb=" CA PRO F 102 " pdb=" N PRO F 102 " pdb=" C PRO F 102 " pdb=" CB PRO F 102 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA PRO D 102 " pdb=" N PRO D 102 " pdb=" C PRO D 102 " pdb=" CB PRO D 102 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA PRO B 102 " pdb=" N PRO B 102 " pdb=" C PRO B 102 " pdb=" CB PRO B 102 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 2751 not shown) Planarity restraints: 2913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 138 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C VAL F 138 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL F 138 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU F 139 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS E 56 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.02e+00 pdb=" C CYS E 56 " -0.042 2.00e-02 2.50e+03 pdb=" O CYS E 56 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG E 57 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 135 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C GLY E 135 " -0.042 2.00e-02 2.50e+03 pdb=" O GLY E 135 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS E 136 " 0.014 2.00e-02 2.50e+03 ... (remaining 2910 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 40 2.44 - 3.05: 10378 3.05 - 3.67: 24856 3.67 - 4.28: 37378 4.28 - 4.90: 62441 Nonbonded interactions: 135093 Sorted by model distance: nonbonded pdb=" NZ LYS B 54 " pdb=" OE1 GLU C 250 " model vdw 1.823 3.120 nonbonded pdb=" OG1 THR H 67 " pdb="MG MG H 301 " model vdw 1.829 2.170 nonbonded pdb=" OG1 THR G 67 " pdb="MG MG G 301 " model vdw 1.874 2.170 nonbonded pdb=" NZ LYS G 103 " pdb=" OP2 DT I 19 " model vdw 1.903 3.120 nonbonded pdb=" S1G AGS G 300 " pdb="MG MG G 301 " model vdw 2.073 2.530 ... (remaining 135088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 19 through 275) selection = (chain 'C' and resid 19 through 275) selection = (chain 'D' and resid 19 through 275) selection = (chain 'E' and resid 19 through 275) selection = (chain 'F' and resid 19 through 275) selection = (chain 'G' and resid 19 through 275) selection = (chain 'H' and resid 19 through 275) } 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: 1.050 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.930 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 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 : 0.014 0.125 17971 Z= 0.985 Angle : 1.527 10.550 24383 Z= 1.224 Chirality : 0.100 0.390 2754 Planarity : 0.006 0.057 2913 Dihedral : 17.058 179.790 7254 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.45 % Allowed : 3.07 % Favored : 96.48 % 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: -0.49 (0.17), residues: 2040 helix: -0.32 (0.13), residues: 1176 sheet: -0.04 (0.51), residues: 96 loop : -0.07 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.007 0.000 TYR C 75 PHE 0.007 0.001 PHE F 125 TRP 0.021 0.001 TRP G 45 HIS 0.001 0.000 HIS F 77 Details of bonding type rmsd covalent geometry : bond 0.01371 (17971) covalent geometry : angle 1.52713 (24383) hydrogen bonds : bond 0.23060 ( 828) hydrogen bonds : angle 7.16223 ( 2458) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 499 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.7162 (mt0) cc_final: 0.6953 (mt0) REVERT: B 66 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7315 (mtmt) REVERT: C 129 THR cc_start: 0.8179 (m) cc_final: 0.7972 (m) REVERT: C 188 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7248 (mm-30) REVERT: D 129 THR cc_start: 0.7824 (m) cc_final: 0.7624 (m) REVERT: D 188 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7072 (mm-30) REVERT: D 223 ASN cc_start: 0.6312 (t0) cc_final: 0.5523 (t0) REVERT: D 246 GLU cc_start: 0.6564 (mt-10) cc_final: 0.6336 (mt-10) REVERT: E 33 ILE cc_start: 0.7764 (mt) cc_final: 0.7557 (mp) REVERT: E 140 MET cc_start: 0.8659 (ttm) cc_final: 0.8234 (ttm) REVERT: E 188 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7226 (mm-30) REVERT: E 275 TYR cc_start: 0.8061 (m-80) cc_final: 0.7572 (m-80) REVERT: F 66 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.5817 (ttpt) REVERT: F 112 TYR cc_start: 0.8542 (t80) cc_final: 0.8053 (t80) REVERT: F 188 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7421 (mm-30) REVERT: G 140 MET cc_start: 0.8814 (ttm) cc_final: 0.8531 (ttm) REVERT: G 188 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7500 (mm-30) REVERT: G 229 MET cc_start: 0.7094 (mtm) cc_final: 0.6870 (mtp) outliers start: 8 outliers final: 2 residues processed: 506 average time/residue: 0.2456 time to fit residues: 160.9346 Evaluate side-chains 254 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 250 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain F residue 66 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN C 37 GLN C 98 GLN C 213 GLN C 269 GLN D 77 HIS E 98 GLN F 98 GLN G 37 GLN H 37 GLN H 206 ASN H 269 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.191614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.153142 restraints weight = 20862.596| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.67 r_work: 0.3672 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17971 Z= 0.150 Angle : 0.574 10.074 24383 Z= 0.317 Chirality : 0.042 0.194 2754 Planarity : 0.005 0.066 2913 Dihedral : 18.558 177.706 2948 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.23 % Allowed : 8.37 % Favored : 89.40 % 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: 1.20 (0.18), residues: 2040 helix: 1.34 (0.15), residues: 1192 sheet: 0.09 (0.52), residues: 96 loop : 0.16 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 258 TYR 0.014 0.001 TYR D 112 PHE 0.027 0.002 PHE B 125 TRP 0.013 0.002 TRP G 211 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00322 (17971) covalent geometry : angle 0.57359 (24383) hydrogen bonds : bond 0.05594 ( 828) hydrogen bonds : angle 4.60137 ( 2458) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 295 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 184 GLU cc_start: 0.8254 (tt0) cc_final: 0.7982 (pt0) REVERT: A 213 GLN cc_start: 0.7837 (mt0) cc_final: 0.7281 (mt0) REVERT: B 85 ARG cc_start: 0.5815 (mtt180) cc_final: 0.5356 (mtt180) REVERT: B 129 THR cc_start: 0.8504 (m) cc_final: 0.8232 (m) REVERT: B 217 LYS cc_start: 0.7123 (mmtt) cc_final: 0.6442 (mmtp) REVERT: B 261 LYS cc_start: 0.6886 (mttm) cc_final: 0.5876 (mmmt) REVERT: C 76 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.6223 (ttp-170) REVERT: C 188 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7939 (mm-30) REVERT: C 203 ASP cc_start: 0.8059 (m-30) cc_final: 0.7440 (t0) REVERT: D 75 TYR cc_start: 0.7484 (m-80) cc_final: 0.7050 (m-80) REVERT: D 188 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7789 (mm-30) REVERT: D 265 LYS cc_start: 0.7058 (ttmm) cc_final: 0.6540 (ttmt) REVERT: E 75 TYR cc_start: 0.6694 (m-10) cc_final: 0.6326 (m-10) REVERT: E 181 LYS cc_start: 0.8066 (mttt) cc_final: 0.7832 (mtpp) REVERT: E 188 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8006 (mm-30) REVERT: F 66 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7425 (mtmt) REVERT: F 75 TYR cc_start: 0.6332 (m-10) cc_final: 0.5927 (m-10) REVERT: F 188 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8144 (mm-30) REVERT: F 209 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6908 (pt0) REVERT: G 81 GLN cc_start: 0.6113 (mt0) cc_final: 0.5757 (mt0) REVERT: G 140 MET cc_start: 0.8697 (ttm) cc_final: 0.8233 (ttm) REVERT: G 188 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8201 (mm-30) REVERT: G 231 ARG cc_start: 0.7336 (ttp80) cc_final: 0.6827 (ptt90) REVERT: G 256 LEU cc_start: 0.8311 (mt) cc_final: 0.8000 (mp) REVERT: H 140 MET cc_start: 0.8712 (ttm) cc_final: 0.8037 (ttm) REVERT: H 148 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7788 (ptt180) REVERT: H 196 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8373 (m-80) outliers start: 40 outliers final: 24 residues processed: 328 average time/residue: 0.2134 time to fit residues: 94.0724 Evaluate side-chains 269 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 241 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 264 ASP Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 225 LYS Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain H residue 257 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 34 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 chunk 145 optimal weight: 9.9990 chunk 200 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 158 optimal weight: 0.5980 chunk 144 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 60 optimal weight: 0.0170 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 269 GLN E 81 GLN E 98 GLN E 206 ASN E 213 GLN G 77 HIS ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.192236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.153749 restraints weight = 20908.849| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.64 r_work: 0.3694 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17971 Z= 0.112 Angle : 0.482 9.930 24383 Z= 0.265 Chirality : 0.039 0.153 2754 Planarity : 0.004 0.044 2913 Dihedral : 18.180 177.495 2940 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.95 % Allowed : 10.27 % Favored : 87.78 % 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: 1.87 (0.18), residues: 2040 helix: 1.90 (0.15), residues: 1200 sheet: 0.23 (0.54), residues: 96 loop : 0.41 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 258 TYR 0.011 0.001 TYR H 93 PHE 0.016 0.001 PHE B 125 TRP 0.016 0.001 TRP G 45 HIS 0.003 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00234 (17971) covalent geometry : angle 0.48222 (24383) hydrogen bonds : bond 0.04506 ( 828) hydrogen bonds : angle 4.18093 ( 2458) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 281 time to evaluate : 0.667 Fit side-chains REVERT: A 184 GLU cc_start: 0.8216 (tt0) cc_final: 0.8005 (pt0) REVERT: B 85 ARG cc_start: 0.6160 (mtt180) cc_final: 0.5425 (mtt180) REVERT: B 182 ARG cc_start: 0.7772 (mpt180) cc_final: 0.7320 (mtm-85) REVERT: B 217 LYS cc_start: 0.7119 (mmtt) cc_final: 0.6625 (mmtp) REVERT: B 261 LYS cc_start: 0.6947 (mttm) cc_final: 0.5978 (mmmt) REVERT: C 188 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7888 (mm-30) REVERT: D 75 TYR cc_start: 0.7466 (m-80) cc_final: 0.7156 (m-80) REVERT: D 188 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7852 (mm-30) REVERT: E 188 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7853 (mm-30) REVERT: F 47 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8165 (t0) REVERT: F 188 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7980 (mm-30) REVERT: F 196 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.8258 (t80) REVERT: G 81 GLN cc_start: 0.6092 (mt0) cc_final: 0.5672 (mt0) REVERT: G 140 MET cc_start: 0.8727 (ttm) cc_final: 0.8461 (ttm) REVERT: G 188 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8192 (mm-30) REVERT: G 231 ARG cc_start: 0.7459 (ttp80) cc_final: 0.6956 (ptt90) REVERT: G 238 GLU cc_start: 0.7998 (mp0) cc_final: 0.7788 (mp0) REVERT: G 256 LEU cc_start: 0.8276 (mt) cc_final: 0.8013 (mp) REVERT: H 140 MET cc_start: 0.8766 (ttm) cc_final: 0.8102 (ttm) outliers start: 35 outliers final: 23 residues processed: 304 average time/residue: 0.1918 time to fit residues: 78.7799 Evaluate side-chains 271 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 246 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 255 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 191 optimal weight: 0.0270 chunk 198 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS B 269 GLN C 213 GLN C 269 GLN E 81 GLN E 206 ASN E 213 GLN G 80 GLN H 37 GLN H 206 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.186101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.147182 restraints weight = 20703.401| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.55 r_work: 0.3600 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17971 Z= 0.163 Angle : 0.535 7.713 24383 Z= 0.289 Chirality : 0.042 0.218 2754 Planarity : 0.005 0.037 2913 Dihedral : 17.993 176.838 2934 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.40 % Allowed : 11.22 % Favored : 86.38 % 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: 1.93 (0.19), residues: 2040 helix: 2.10 (0.15), residues: 1200 sheet: 0.07 (0.54), residues: 96 loop : 0.15 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 258 TYR 0.015 0.001 TYR H 93 PHE 0.016 0.002 PHE B 125 TRP 0.012 0.002 TRP G 45 HIS 0.008 0.001 HIS E 77 Details of bonding type rmsd covalent geometry : bond 0.00388 (17971) covalent geometry : angle 0.53506 (24383) hydrogen bonds : bond 0.05087 ( 828) hydrogen bonds : angle 4.12227 ( 2458) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 248 time to evaluate : 0.680 Fit side-chains REVERT: A 170 LEU cc_start: 0.8544 (mt) cc_final: 0.8243 (mp) REVERT: A 184 GLU cc_start: 0.8389 (tt0) cc_final: 0.8027 (pt0) REVERT: B 76 ARG cc_start: 0.7676 (ttm170) cc_final: 0.7419 (mtp180) REVERT: B 182 ARG cc_start: 0.7919 (mpt180) cc_final: 0.7620 (mtt90) REVERT: B 217 LYS cc_start: 0.7419 (mmtt) cc_final: 0.6956 (mmtp) REVERT: B 261 LYS cc_start: 0.7102 (mttm) cc_final: 0.6156 (mmmt) REVERT: C 188 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7977 (mm-30) REVERT: D 188 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7866 (mm-30) REVERT: E 75 TYR cc_start: 0.7251 (m-10) cc_final: 0.6875 (m-10) REVERT: E 188 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8011 (mm-30) REVERT: F 188 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8198 (mm-30) REVERT: G 81 GLN cc_start: 0.5906 (mt0) cc_final: 0.5477 (mt0) REVERT: G 140 MET cc_start: 0.8751 (ttm) cc_final: 0.8387 (ttm) REVERT: G 188 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8241 (mm-30) REVERT: G 256 LEU cc_start: 0.8314 (mt) cc_final: 0.8048 (mp) REVERT: H 140 MET cc_start: 0.8815 (ttm) cc_final: 0.8273 (ttm) REVERT: H 210 MET cc_start: 0.8396 (ptp) cc_final: 0.7974 (ptp) REVERT: H 246 GLU cc_start: 0.6670 (mt-10) cc_final: 0.6415 (mt-10) REVERT: H 275 TYR cc_start: 0.7486 (m-80) cc_final: 0.7253 (m-80) outliers start: 43 outliers final: 29 residues processed: 276 average time/residue: 0.1938 time to fit residues: 73.5994 Evaluate side-chains 250 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 247 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 166 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 176 optimal weight: 0.0050 chunk 189 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 GLN C 269 GLN E 206 ASN H 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.187877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.148480 restraints weight = 20591.976| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.69 r_work: 0.3623 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17971 Z= 0.115 Angle : 0.472 6.874 24383 Z= 0.259 Chirality : 0.039 0.183 2754 Planarity : 0.004 0.038 2913 Dihedral : 17.807 178.004 2934 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.18 % Allowed : 12.39 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.19), residues: 2040 helix: 2.19 (0.15), residues: 1224 sheet: 0.10 (0.55), residues: 96 loop : 0.08 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 258 TYR 0.014 0.001 TYR D 75 PHE 0.016 0.001 PHE B 125 TRP 0.014 0.001 TRP G 45 HIS 0.004 0.001 HIS E 77 Details of bonding type rmsd covalent geometry : bond 0.00257 (17971) covalent geometry : angle 0.47158 (24383) hydrogen bonds : bond 0.04232 ( 828) hydrogen bonds : angle 3.97533 ( 2458) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 237 time to evaluate : 0.698 Fit side-chains REVERT: A 170 LEU cc_start: 0.8419 (mt) cc_final: 0.8196 (mp) REVERT: A 184 GLU cc_start: 0.8418 (tt0) cc_final: 0.8074 (pt0) REVERT: B 76 ARG cc_start: 0.7651 (ttm170) cc_final: 0.7382 (mtp180) REVERT: B 182 ARG cc_start: 0.7867 (mpt180) cc_final: 0.7512 (mtm-85) REVERT: B 217 LYS cc_start: 0.7431 (mmtt) cc_final: 0.7052 (mmtp) REVERT: B 261 LYS cc_start: 0.7114 (mttm) cc_final: 0.6177 (mmmt) REVERT: B 269 GLN cc_start: 0.7481 (mm-40) cc_final: 0.7053 (mm-40) REVERT: C 188 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7971 (mm-30) REVERT: C 210 MET cc_start: 0.8080 (ttm) cc_final: 0.7843 (ptp) REVERT: D 188 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7798 (mm-30) REVERT: E 188 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7999 (mm-30) REVERT: F 119 LYS cc_start: 0.8057 (tttp) cc_final: 0.7784 (tppt) REVERT: F 188 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8064 (mm-30) REVERT: F 196 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8424 (t80) REVERT: G 81 GLN cc_start: 0.6005 (mt0) cc_final: 0.5637 (mt0) REVERT: G 140 MET cc_start: 0.8736 (ttm) cc_final: 0.8404 (ttm) REVERT: G 188 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8258 (mm-30) REVERT: G 231 ARG cc_start: 0.7386 (ttp80) cc_final: 0.6933 (ptt90) REVERT: G 256 LEU cc_start: 0.8336 (mt) cc_final: 0.8065 (mp) REVERT: H 140 MET cc_start: 0.8821 (ttm) cc_final: 0.8200 (ttm) REVERT: H 148 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7689 (ptt180) REVERT: H 210 MET cc_start: 0.8303 (ptp) cc_final: 0.7897 (ptp) outliers start: 39 outliers final: 31 residues processed: 263 average time/residue: 0.1844 time to fit residues: 66.7046 Evaluate side-chains 262 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 255 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 150 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 8 optimal weight: 0.0070 chunk 40 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 188 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 GLN C 269 GLN E 213 GLN H 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.188855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150336 restraints weight = 20519.103| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.61 r_work: 0.3652 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17971 Z= 0.108 Angle : 0.452 6.134 24383 Z= 0.249 Chirality : 0.039 0.156 2754 Planarity : 0.004 0.037 2913 Dihedral : 17.620 178.418 2934 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.18 % Allowed : 12.67 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.19), residues: 2040 helix: 2.28 (0.15), residues: 1224 sheet: 0.27 (0.57), residues: 96 loop : 0.11 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 258 TYR 0.008 0.001 TYR H 93 PHE 0.015 0.001 PHE B 125 TRP 0.012 0.001 TRP E 45 HIS 0.004 0.001 HIS E 77 Details of bonding type rmsd covalent geometry : bond 0.00238 (17971) covalent geometry : angle 0.45189 (24383) hydrogen bonds : bond 0.03783 ( 828) hydrogen bonds : angle 3.88747 ( 2458) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 247 time to evaluate : 0.699 Fit side-chains REVERT: A 107 LYS cc_start: 0.8551 (tttm) cc_final: 0.8126 (ttpp) REVERT: A 170 LEU cc_start: 0.8320 (mt) cc_final: 0.8086 (mp) REVERT: A 213 GLN cc_start: 0.7385 (mt0) cc_final: 0.7137 (mt0) REVERT: B 76 ARG cc_start: 0.7614 (ttm170) cc_final: 0.7347 (mtp180) REVERT: B 182 ARG cc_start: 0.7834 (mpt180) cc_final: 0.7516 (mtm-85) REVERT: C 188 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7916 (mm-30) REVERT: C 261 LYS cc_start: 0.5980 (mmtp) cc_final: 0.5584 (mmmt) REVERT: D 188 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7937 (mm-30) REVERT: E 188 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7937 (mm-30) REVERT: F 119 LYS cc_start: 0.8034 (tttp) cc_final: 0.7761 (tppt) REVERT: F 188 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8025 (mm-30) REVERT: F 196 PHE cc_start: 0.9297 (OUTLIER) cc_final: 0.8436 (t80) REVERT: G 81 GLN cc_start: 0.5991 (mt0) cc_final: 0.5644 (mt0) REVERT: G 140 MET cc_start: 0.8756 (ttm) cc_final: 0.8406 (ttm) REVERT: G 188 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8226 (mm-30) REVERT: G 231 ARG cc_start: 0.7459 (ttp80) cc_final: 0.6992 (ptt90) REVERT: G 238 GLU cc_start: 0.8043 (mp0) cc_final: 0.7782 (mp0) REVERT: G 256 LEU cc_start: 0.8319 (mt) cc_final: 0.8055 (mp) REVERT: H 140 MET cc_start: 0.8801 (ttm) cc_final: 0.8212 (ttm) REVERT: H 148 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7631 (ptt180) REVERT: H 210 MET cc_start: 0.8312 (ptp) cc_final: 0.7907 (ptp) outliers start: 39 outliers final: 36 residues processed: 271 average time/residue: 0.1979 time to fit residues: 73.7508 Evaluate side-chains 260 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 264 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 255 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 71 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 GLN C 269 GLN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.186595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147488 restraints weight = 20688.331| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.65 r_work: 0.3603 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17971 Z= 0.136 Angle : 0.489 6.693 24383 Z= 0.266 Chirality : 0.040 0.189 2754 Planarity : 0.004 0.036 2913 Dihedral : 17.613 178.249 2934 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.23 % Allowed : 13.23 % 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: 2.04 (0.19), residues: 2040 helix: 2.25 (0.15), residues: 1224 sheet: -0.06 (0.48), residues: 128 loop : 0.06 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 249 TYR 0.011 0.001 TYR H 93 PHE 0.014 0.002 PHE B 125 TRP 0.012 0.001 TRP G 45 HIS 0.005 0.001 HIS E 77 Details of bonding type rmsd covalent geometry : bond 0.00318 (17971) covalent geometry : angle 0.48947 (24383) hydrogen bonds : bond 0.04238 ( 828) hydrogen bonds : angle 3.95171 ( 2458) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 0.704 Fit side-chains REVERT: A 107 LYS cc_start: 0.8557 (tttm) cc_final: 0.8139 (ttpp) REVERT: A 170 LEU cc_start: 0.8438 (mt) cc_final: 0.8203 (mp) REVERT: B 76 ARG cc_start: 0.7683 (ttm170) cc_final: 0.7414 (mtp180) REVERT: B 182 ARG cc_start: 0.7871 (mpt180) cc_final: 0.7525 (mtm-85) REVERT: B 217 LYS cc_start: 0.7716 (mmmt) cc_final: 0.6473 (mmtp) REVERT: B 269 GLN cc_start: 0.7726 (mm-40) cc_final: 0.6983 (mm-40) REVERT: C 188 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7955 (mm-30) REVERT: C 261 LYS cc_start: 0.6012 (mmtp) cc_final: 0.5638 (mmmt) REVERT: D 188 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7880 (mm-30) REVERT: E 188 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8004 (mm-30) REVERT: F 119 LYS cc_start: 0.8028 (tttp) cc_final: 0.7748 (tppt) REVERT: F 188 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8204 (mm-30) REVERT: F 196 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8405 (t80) REVERT: G 81 GLN cc_start: 0.6004 (mt0) cc_final: 0.5673 (mt0) REVERT: G 188 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8249 (mm-30) REVERT: G 238 GLU cc_start: 0.8097 (mp0) cc_final: 0.7844 (mp0) REVERT: G 256 LEU cc_start: 0.8328 (mt) cc_final: 0.8072 (mp) REVERT: H 140 MET cc_start: 0.8819 (ttm) cc_final: 0.8208 (ttm) REVERT: H 148 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7591 (ptt180) REVERT: H 210 MET cc_start: 0.8303 (ptp) cc_final: 0.7881 (ptp) REVERT: H 246 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6273 (mt-10) outliers start: 40 outliers final: 36 residues processed: 250 average time/residue: 0.1939 time to fit residues: 66.3201 Evaluate side-chains 259 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 255 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 111 optimal weight: 0.4980 chunk 201 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 137 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 156 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 GLN C 269 GLN E 213 GLN H 37 GLN H 77 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.187672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.148735 restraints weight = 20605.030| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.69 r_work: 0.3619 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17971 Z= 0.111 Angle : 0.460 6.630 24383 Z= 0.252 Chirality : 0.039 0.164 2754 Planarity : 0.004 0.036 2913 Dihedral : 17.485 178.937 2934 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.06 % Allowed : 13.39 % 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: 2.08 (0.19), residues: 2040 helix: 2.29 (0.15), residues: 1224 sheet: -0.04 (0.49), residues: 128 loop : 0.06 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 258 TYR 0.008 0.001 TYR H 93 PHE 0.014 0.001 PHE B 125 TRP 0.012 0.001 TRP E 45 HIS 0.003 0.001 HIS E 77 Details of bonding type rmsd covalent geometry : bond 0.00249 (17971) covalent geometry : angle 0.45994 (24383) hydrogen bonds : bond 0.03821 ( 828) hydrogen bonds : angle 3.88818 ( 2458) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 233 time to evaluate : 0.740 Fit side-chains REVERT: A 107 LYS cc_start: 0.8554 (tttm) cc_final: 0.8134 (ttpp) REVERT: A 170 LEU cc_start: 0.8370 (mt) cc_final: 0.8107 (mp) REVERT: A 188 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7930 (mm-30) REVERT: A 213 GLN cc_start: 0.7345 (mt0) cc_final: 0.7016 (mt0) REVERT: B 182 ARG cc_start: 0.7862 (mpt180) cc_final: 0.7525 (mtm-85) REVERT: B 217 LYS cc_start: 0.7635 (mmmt) cc_final: 0.6583 (mmtp) REVERT: B 269 GLN cc_start: 0.7473 (mm-40) cc_final: 0.6811 (mm-40) REVERT: C 188 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7954 (mm-30) REVERT: C 246 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6688 (mt-10) REVERT: C 261 LYS cc_start: 0.6023 (mmtp) cc_final: 0.5673 (mmmt) REVERT: D 85 ARG cc_start: 0.5859 (mtt180) cc_final: 0.5390 (mmm160) REVERT: D 188 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7839 (mm-30) REVERT: E 188 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8013 (mm-30) REVERT: F 119 LYS cc_start: 0.8079 (tttp) cc_final: 0.7747 (tppt) REVERT: F 188 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8252 (mm-30) REVERT: F 196 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8427 (t80) REVERT: G 81 GLN cc_start: 0.6003 (mt0) cc_final: 0.5608 (mt0) REVERT: G 140 MET cc_start: 0.8783 (ttm) cc_final: 0.8527 (ttm) REVERT: G 188 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8268 (mm-30) REVERT: G 238 GLU cc_start: 0.7968 (mp0) cc_final: 0.7732 (mp0) REVERT: G 256 LEU cc_start: 0.8344 (mt) cc_final: 0.8082 (mp) REVERT: H 140 MET cc_start: 0.8783 (ttm) cc_final: 0.8155 (ttm) REVERT: H 148 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7556 (ptt180) REVERT: H 210 MET cc_start: 0.8267 (ptp) cc_final: 0.7825 (ptp) REVERT: H 246 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6349 (mt-10) outliers start: 37 outliers final: 34 residues processed: 257 average time/residue: 0.1990 time to fit residues: 70.0257 Evaluate side-chains 255 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 255 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 142 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 197 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 26 optimal weight: 0.0010 chunk 168 optimal weight: 2.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN C 269 GLN H 37 GLN H 206 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.185724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.146161 restraints weight = 20739.566| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.68 r_work: 0.3601 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17971 Z= 0.135 Angle : 0.492 6.612 24383 Z= 0.266 Chirality : 0.040 0.189 2754 Planarity : 0.004 0.035 2913 Dihedral : 17.497 178.656 2934 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.18 % Allowed : 13.28 % 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: 2.01 (0.19), residues: 2040 helix: 2.27 (0.15), residues: 1224 sheet: -0.18 (0.48), residues: 128 loop : -0.05 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 76 TYR 0.012 0.001 TYR H 93 PHE 0.013 0.002 PHE E 125 TRP 0.012 0.001 TRP G 45 HIS 0.005 0.001 HIS E 77 Details of bonding type rmsd covalent geometry : bond 0.00315 (17971) covalent geometry : angle 0.49201 (24383) hydrogen bonds : bond 0.04329 ( 828) hydrogen bonds : angle 3.95647 ( 2458) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 0.547 Fit side-chains REVERT: A 107 LYS cc_start: 0.8560 (tttm) cc_final: 0.8139 (ttpp) REVERT: A 188 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7928 (mm-30) REVERT: B 182 ARG cc_start: 0.7855 (mpt180) cc_final: 0.7548 (mtm-85) REVERT: B 217 LYS cc_start: 0.7494 (mmmt) cc_final: 0.6635 (mmtp) REVERT: B 229 MET cc_start: 0.6241 (mtt) cc_final: 0.5872 (mtt) REVERT: B 269 GLN cc_start: 0.7513 (mm-40) cc_final: 0.6873 (mm-40) REVERT: C 188 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7931 (mm-30) REVERT: C 246 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6879 (mt-10) REVERT: C 261 LYS cc_start: 0.6062 (mmtp) cc_final: 0.5648 (mmmt) REVERT: D 85 ARG cc_start: 0.5835 (mtt180) cc_final: 0.5417 (mmm160) REVERT: D 119 LYS cc_start: 0.7595 (tttm) cc_final: 0.7388 (ttpp) REVERT: D 188 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7907 (mm-30) REVERT: D 258 ARG cc_start: 0.7432 (mtp85) cc_final: 0.6316 (mtt90) REVERT: E 188 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8013 (mm-30) REVERT: F 119 LYS cc_start: 0.7975 (tttp) cc_final: 0.7690 (tppt) REVERT: F 188 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8245 (mm-30) REVERT: F 196 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8371 (t80) REVERT: F 260 LEU cc_start: 0.7739 (mp) cc_final: 0.7383 (mp) REVERT: G 81 GLN cc_start: 0.5975 (mt0) cc_final: 0.5649 (mt0) REVERT: G 140 MET cc_start: 0.8798 (ttm) cc_final: 0.8506 (ttm) REVERT: G 188 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8228 (mm-30) REVERT: G 238 GLU cc_start: 0.7940 (mp0) cc_final: 0.7702 (mp0) REVERT: G 256 LEU cc_start: 0.8330 (mt) cc_final: 0.8073 (mp) REVERT: H 140 MET cc_start: 0.8804 (ttm) cc_final: 0.8177 (ttm) REVERT: H 210 MET cc_start: 0.8256 (ptp) cc_final: 0.7812 (ptp) REVERT: H 246 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6268 (mt-10) outliers start: 39 outliers final: 34 residues processed: 248 average time/residue: 0.1812 time to fit residues: 61.9266 Evaluate side-chains 252 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 255 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 143 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 171 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN C 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.184997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145905 restraints weight = 20686.193| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.62 r_work: 0.3601 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17971 Z= 0.145 Angle : 0.502 7.203 24383 Z= 0.271 Chirality : 0.040 0.199 2754 Planarity : 0.004 0.037 2913 Dihedral : 17.520 178.944 2934 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.12 % Allowed : 13.67 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.93 (0.19), residues: 2040 helix: 2.23 (0.15), residues: 1224 sheet: -0.24 (0.48), residues: 128 loop : -0.11 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 76 TYR 0.011 0.001 TYR H 93 PHE 0.015 0.002 PHE E 125 TRP 0.012 0.001 TRP G 45 HIS 0.005 0.001 HIS F 77 Details of bonding type rmsd covalent geometry : bond 0.00344 (17971) covalent geometry : angle 0.50161 (24383) hydrogen bonds : bond 0.04419 ( 828) hydrogen bonds : angle 3.97404 ( 2458) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 219 time to evaluate : 0.688 Fit side-chains REVERT: A 188 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7892 (mm-30) REVERT: A 213 GLN cc_start: 0.7367 (mt0) cc_final: 0.7016 (mt0) REVERT: B 76 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7585 (mtp180) REVERT: B 182 ARG cc_start: 0.7859 (mpt180) cc_final: 0.7555 (mtm-85) REVERT: B 217 LYS cc_start: 0.7645 (mmmt) cc_final: 0.6843 (mmtp) REVERT: B 229 MET cc_start: 0.6313 (mtt) cc_final: 0.5923 (mtt) REVERT: B 269 GLN cc_start: 0.7537 (mm-40) cc_final: 0.6879 (mm-40) REVERT: C 85 ARG cc_start: 0.6040 (OUTLIER) cc_final: 0.4315 (mmt180) REVERT: C 188 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7924 (mm-30) REVERT: C 246 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6734 (mt-10) REVERT: C 261 LYS cc_start: 0.6071 (mmtp) cc_final: 0.5654 (mmmt) REVERT: D 85 ARG cc_start: 0.5825 (mtt180) cc_final: 0.5440 (mmm160) REVERT: D 119 LYS cc_start: 0.7550 (tttm) cc_final: 0.7348 (ttpp) REVERT: D 188 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7903 (mm-30) REVERT: D 258 ARG cc_start: 0.7593 (mtp85) cc_final: 0.6485 (mtt90) REVERT: E 188 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7998 (mm-30) REVERT: E 261 LYS cc_start: 0.6534 (mmtm) cc_final: 0.6326 (mmtm) REVERT: F 119 LYS cc_start: 0.7881 (tttp) cc_final: 0.7657 (tppt) REVERT: F 188 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8229 (mm-30) REVERT: F 196 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8367 (t80) REVERT: F 238 GLU cc_start: 0.8139 (mp0) cc_final: 0.7829 (mp0) REVERT: F 260 LEU cc_start: 0.7754 (mp) cc_final: 0.7406 (mp) REVERT: G 81 GLN cc_start: 0.5952 (mt0) cc_final: 0.5627 (mt0) REVERT: G 140 MET cc_start: 0.8810 (ttm) cc_final: 0.8539 (ttm) REVERT: G 238 GLU cc_start: 0.7817 (mp0) cc_final: 0.7556 (mp0) REVERT: G 256 LEU cc_start: 0.8349 (mt) cc_final: 0.8089 (mp) REVERT: H 140 MET cc_start: 0.8780 (ttm) cc_final: 0.8168 (ttm) REVERT: H 210 MET cc_start: 0.8238 (ptp) cc_final: 0.7800 (ptp) outliers start: 38 outliers final: 33 residues processed: 240 average time/residue: 0.1810 time to fit residues: 60.0870 Evaluate side-chains 251 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 255 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 91 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 200 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN C 269 GLN H 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.184066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145521 restraints weight = 20798.366| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.63 r_work: 0.3579 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17971 Z= 0.148 Angle : 0.513 7.610 24383 Z= 0.278 Chirality : 0.041 0.204 2754 Planarity : 0.004 0.040 2913 Dihedral : 17.583 179.352 2934 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.23 % Allowed : 13.62 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.85 (0.19), residues: 2040 helix: 2.21 (0.15), residues: 1224 sheet: -0.22 (0.35), residues: 208 loop : -0.24 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 76 TYR 0.012 0.001 TYR H 93 PHE 0.015 0.002 PHE E 125 TRP 0.012 0.001 TRP F 20 HIS 0.005 0.001 HIS F 77 Details of bonding type rmsd covalent geometry : bond 0.00352 (17971) covalent geometry : angle 0.51286 (24383) hydrogen bonds : bond 0.04578 ( 828) hydrogen bonds : angle 4.01461 ( 2458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5021.53 seconds wall clock time: 86 minutes 28.21 seconds (5188.21 seconds total)