Starting phenix.real_space_refine on Sat Jul 4 02:03:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m99_23720/07_2026/7m99_23720.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m99_23720/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7m99_23720/07_2026/7m99_23720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m99_23720/07_2026/7m99_23720.map" model { file = "/net/cci-nas-00/data/ceres_data/7m99_23720/07_2026/7m99_23720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m99_23720/07_2026/7m99_23720.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7m99_23720/07_2026/7m99_23720.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m99_23720/07_2026/7m99_23720.cif" } 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-6108/lib/python3.11/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: 3.92, per 1000 atoms: 0.22 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: 1.59 Conformation dependent library (CDL) restraints added in 702.7 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: 1.84 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: 2.73 Time building geometry restraints manager: 2.08 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: 20168 2.11 - 4.22: 3872 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: 10645 35.96 - 71.92: 342 71.92 - 107.87: 31 107.87 - 143.83: 5 143.83 - 179.79: 10 Dihedral angle restraints: 11033 sinusoidal: 5073 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 11030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1333 0.078 - 0.156: 1115 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 17.580 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 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= 0.997 Angle : 1.537 10.550 24383 Z= 1.243 Chirality : 0.101 0.390 2754 Planarity : 0.006 0.057 2913 Dihedral : 16.751 179.790 7177 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/Z covalent geometry : bond 0.01378 / 1.00 (17971) covalent geometry : angle 1.53718 / 1.24 (24383) hydrogen bonds : bond 0.23060 / 15.41 ( 828) hydrogen bonds : angle 7.16223 / 5.12 ( 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 : 0.632 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: 0.2354 time to fit residues: 155.4194 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 : 0.718 ------------------------------------------------------------------------------- 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: 30.0000 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... 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 Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.192222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.155636 restraints weight = 21092.629| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.51 r_work: 0.3686 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17971 Z= 0.160 Angle : 0.600 10.072 24383 Z= 0.334 Chirality : 0.042 0.238 2754 Planarity : 0.006 0.075 2913 Dihedral : 18.246 176.719 2871 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.29 % Allowed : 8.98 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.02 (0.18), residues: 2040 helix: 1.16 (0.14), residues: 1192 sheet: -0.01 (0.51), residues: 96 loop : 0.16 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 76 TYR 0.014 0.001 TYR D 112 PHE 0.021 0.002 PHE B 125 TRP 0.016 0.002 TRP G 211 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (17971) covalent geometry : angle 0.59972 / 0.33 (24383) hydrogen bonds : bond 0.06589 / 4.37 ( 828) hydrogen bonds : angle 4.82703 / 3.47 ( 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 327 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 286 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7093 (ttpp) cc_final: 0.6866 (ttpp) REVERT: A 184 GLU cc_start: 0.8251 (tt0) cc_final: 0.7746 (pt0) REVERT: A 213 GLN cc_start: 0.7766 (mt0) cc_final: 0.7272 (mt0) REVERT: B 129 THR cc_start: 0.8409 (m) cc_final: 0.8165 (m) REVERT: B 217 LYS cc_start: 0.7077 (mmtt) cc_final: 0.6386 (mmtp) REVERT: B 261 LYS cc_start: 0.6890 (mttm) cc_final: 0.5890 (mmmt) REVERT: C 76 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.6321 (ttp-170) REVERT: C 188 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7954 (mm-30) REVERT: C 203 ASP cc_start: 0.7984 (m-30) cc_final: 0.7415 (t0) REVERT: D 75 TYR cc_start: 0.7574 (m-80) cc_final: 0.7275 (m-80) REVERT: D 188 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7799 (mm-30) REVERT: D 265 LYS cc_start: 0.7018 (ttmm) cc_final: 0.6798 (ttmt) REVERT: E 181 LYS cc_start: 0.8136 (mttt) cc_final: 0.7908 (mtpp) REVERT: E 188 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8037 (mm-30) REVERT: E 222 SER cc_start: 0.7452 (m) cc_final: 0.7220 (m) REVERT: F 188 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8165 (mm-30) REVERT: G 81 GLN cc_start: 0.6087 (mt0) cc_final: 0.5718 (mt0) REVERT: G 140 MET cc_start: 0.8644 (ttm) cc_final: 0.8130 (ttm) REVERT: G 188 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8176 (mm-30) REVERT: G 246 GLU cc_start: 0.6659 (mt-10) cc_final: 0.6436 (mt-10) REVERT: G 256 LEU cc_start: 0.8410 (mt) cc_final: 0.8179 (mp) REVERT: H 140 MET cc_start: 0.8622 (ttm) cc_final: 0.7947 (ttm) REVERT: H 148 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7709 (ptt180) outliers start: 41 outliers final: 24 residues processed: 321 average time/residue: 0.2090 time to fit residues: 90.7413 Evaluate side-chains 262 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 B residue 123 SER Chi-restraints excluded: chain B residue 222 SER 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 123 SER 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 123 SER Chi-restraints excluded: chain E residue 127 ASP 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 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 255 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: 0.3980 chunk 145 optimal weight: 5.9990 chunk 200 optimal weight: 30.0000 chunk 52 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 223 ASN B 269 GLN C 213 GLN C 269 GLN E 81 GLN E 98 GLN E 206 ASN E 213 GLN F 206 ASN G 37 GLN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.184996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144870 restraints weight = 20845.604| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.80 r_work: 0.3578 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17971 Z= 0.201 Angle : 0.614 10.545 24383 Z= 0.336 Chirality : 0.045 0.258 2754 Planarity : 0.006 0.045 2913 Dihedral : 18.237 177.728 2859 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.23 % Allowed : 10.16 % Favored : 87.61 % 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: 1.30 (0.18), residues: 2040 helix: 1.57 (0.15), residues: 1200 sheet: -0.43 (0.49), residues: 96 loop : -0.01 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 148 TYR 0.009 0.002 TYR D 112 PHE 0.020 0.002 PHE E 125 TRP 0.018 0.002 TRP G 45 HIS 0.008 0.002 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (17971) covalent geometry : angle 0.61404 / 0.34 (24383) hydrogen bonds : bond 0.06290 / 4.23 ( 828) hydrogen bonds : angle 4.43981 / 3.18 ( 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 298 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 258 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 184 GLU cc_start: 0.8358 (tt0) cc_final: 0.8086 (pt0) REVERT: B 182 ARG cc_start: 0.7270 (mtt90) cc_final: 0.7013 (mtm-85) REVERT: B 217 LYS cc_start: 0.7347 (mmtt) cc_final: 0.6610 (mmtp) REVERT: B 261 LYS cc_start: 0.6914 (mttm) cc_final: 0.5928 (mmmt) REVERT: C 188 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8085 (mm-30) REVERT: D 188 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7816 (mm-30) REVERT: D 265 LYS cc_start: 0.7460 (ttmm) cc_final: 0.7235 (mtpt) REVERT: E 29 LYS cc_start: 0.7587 (pttp) cc_final: 0.7382 (pttp) REVERT: E 188 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7977 (mm-30) REVERT: F 188 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8206 (mm-30) REVERT: G 81 GLN cc_start: 0.6080 (mt0) cc_final: 0.5722 (mt0) REVERT: G 140 MET cc_start: 0.8800 (ttm) cc_final: 0.8391 (ttm) REVERT: G 188 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8335 (mm-30) REVERT: G 231 ARG cc_start: 0.7355 (ttp80) cc_final: 0.6825 (ptt90) REVERT: G 235 SER cc_start: 0.7406 (m) cc_final: 0.7178 (m) REVERT: G 256 LEU cc_start: 0.8298 (mt) cc_final: 0.8046 (mp) REVERT: H 140 MET cc_start: 0.8804 (ttm) cc_final: 0.8157 (ttm) REVERT: H 210 MET cc_start: 0.8025 (ptm) cc_final: 0.7802 (ptm) outliers start: 40 outliers final: 27 residues processed: 289 average time/residue: 0.1974 time to fit residues: 78.3163 Evaluate side-chains 254 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 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 C residue 114 LYS 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 C residue 181 LYS Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 123 SER 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 47 ASP Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 124 ASP 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: 2.9990 chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 198 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 0.0040 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 269 GLN C 77 HIS C 269 GLN D 77 HIS E 206 ASN G 77 HIS H 37 GLN H 206 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.186757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.147466 restraints weight = 20697.092| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.69 r_work: 0.3618 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3650 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= 0.138 Angle : 0.511 10.200 24383 Z= 0.283 Chirality : 0.041 0.257 2754 Planarity : 0.005 0.040 2913 Dihedral : 18.058 175.194 2857 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.40 % Allowed : 11.50 % Favored : 86.10 % 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: 1.67 (0.18), residues: 2040 helix: 1.94 (0.15), residues: 1200 sheet: -0.74 (0.44), residues: 136 loop : 0.14 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 243 TYR 0.013 0.001 TYR D 75 PHE 0.018 0.002 PHE B 125 TRP 0.016 0.001 TRP G 45 HIS 0.005 0.001 HIS E 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (17971) covalent geometry : angle 0.51106 / 0.28 (24383) hydrogen bonds : bond 0.05009 / 3.34 ( 828) hydrogen bonds : angle 4.16837 / 2.98 ( 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 295 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 252 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 184 GLU cc_start: 0.8408 (tt0) cc_final: 0.8009 (pt0) REVERT: A 262 LYS cc_start: 0.5549 (pttt) cc_final: 0.5083 (ptpt) REVERT: B 76 ARG cc_start: 0.7609 (ttm170) cc_final: 0.7381 (mtp180) REVERT: B 181 LYS cc_start: 0.8487 (pttp) cc_final: 0.8095 (ptpt) REVERT: B 182 ARG cc_start: 0.7263 (mtt90) cc_final: 0.6976 (mtm-85) REVERT: B 217 LYS cc_start: 0.7310 (mmtt) cc_final: 0.6810 (mmtp) REVERT: B 261 LYS cc_start: 0.6945 (mttm) cc_final: 0.6004 (mmmt) REVERT: C 188 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7953 (mm-30) REVERT: C 210 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7945 (ptp) REVERT: D 188 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7735 (mm-30) REVERT: D 223 ASN cc_start: 0.6989 (p0) cc_final: 0.6495 (p0) REVERT: D 265 LYS cc_start: 0.7531 (ttmm) cc_final: 0.7257 (mtpt) REVERT: E 188 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7979 (mm-30) REVERT: F 188 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8127 (mm-30) REVERT: F 196 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.8429 (t80) REVERT: G 81 GLN cc_start: 0.5923 (mt0) cc_final: 0.5563 (mt0) REVERT: G 140 MET cc_start: 0.8764 (ttm) cc_final: 0.8430 (ttm) REVERT: G 188 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8231 (mm-30) REVERT: G 231 ARG cc_start: 0.7498 (ttp80) cc_final: 0.6974 (ptt90) REVERT: G 256 LEU cc_start: 0.8281 (mt) cc_final: 0.8002 (mp) REVERT: G 275 TYR cc_start: 0.7863 (m-80) cc_final: 0.7445 (m-80) REVERT: H 140 MET cc_start: 0.8864 (ttm) cc_final: 0.8222 (ttm) REVERT: H 210 MET cc_start: 0.8050 (ptm) cc_final: 0.7812 (ptm) outliers start: 43 outliers final: 34 residues processed: 277 average time/residue: 0.1960 time to fit residues: 74.5386 Evaluate side-chains 267 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 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 181 LYS Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 224 LEU 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 196 PHE 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 55 SER Chi-restraints excluded: chain G residue 124 ASP 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 200 SER Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 257 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 166 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 110 optimal weight: 0.2980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS B 269 GLN D 77 HIS E 206 ASN G 77 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.185374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.146538 restraints weight = 20610.823| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.66 r_work: 0.3594 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17971 Z= 0.144 Angle : 0.516 9.984 24383 Z= 0.283 Chirality : 0.042 0.262 2754 Planarity : 0.004 0.040 2913 Dihedral : 18.027 179.315 2857 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.57 % Allowed : 12.33 % Favored : 85.10 % 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: 1.75 (0.19), residues: 2040 helix: 2.08 (0.15), residues: 1200 sheet: -0.80 (0.44), residues: 136 loop : 0.05 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 50 TYR 0.010 0.001 TYR H 93 PHE 0.016 0.002 PHE B 125 TRP 0.014 0.002 TRP G 45 HIS 0.006 0.001 HIS E 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (17971) covalent geometry : angle 0.51592 / 0.28 (24383) hydrogen bonds : bond 0.04943 / 3.32 ( 828) hydrogen bonds : angle 4.10954 / 2.93 ( 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 282 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 0.721 Fit side-chains REVERT: A 76 ARG cc_start: 0.7400 (ttm170) cc_final: 0.7046 (mtp180) REVERT: A 184 GLU cc_start: 0.8461 (tt0) cc_final: 0.8014 (pt0) REVERT: A 210 MET cc_start: 0.7611 (ttm) cc_final: 0.7285 (ptm) REVERT: A 262 LYS cc_start: 0.5383 (pttt) cc_final: 0.4996 (ptpt) REVERT: B 181 LYS cc_start: 0.8516 (pttp) cc_final: 0.8078 (ptpt) REVERT: B 182 ARG cc_start: 0.7341 (mtt90) cc_final: 0.7098 (mtm-85) REVERT: B 217 LYS cc_start: 0.7443 (mmtt) cc_final: 0.7018 (mmtp) REVERT: B 261 LYS cc_start: 0.7052 (mttm) cc_final: 0.6155 (mmmt) REVERT: C 85 ARG cc_start: 0.5935 (OUTLIER) cc_final: 0.5391 (mmt180) REVERT: C 188 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7978 (mm-30) REVERT: D 74 ARG cc_start: 0.7999 (ttp-170) cc_final: 0.7666 (ptm160) REVERT: D 188 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7811 (mm-30) REVERT: D 223 ASN cc_start: 0.7004 (p0) cc_final: 0.6740 (p0) REVERT: D 265 LYS cc_start: 0.7514 (ttmm) cc_final: 0.7256 (mtpt) REVERT: E 188 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7977 (mm-30) REVERT: F 188 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8172 (mm-30) REVERT: F 196 PHE cc_start: 0.9322 (OUTLIER) cc_final: 0.8485 (t80) REVERT: G 81 GLN cc_start: 0.6027 (mt0) cc_final: 0.5691 (mt0) REVERT: G 188 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8244 (mm-30) REVERT: G 256 LEU cc_start: 0.8295 (mt) cc_final: 0.8028 (mp) REVERT: G 275 TYR cc_start: 0.7866 (m-80) cc_final: 0.7504 (m-80) REVERT: H 140 MET cc_start: 0.8866 (ttm) cc_final: 0.8220 (ttm) REVERT: H 210 MET cc_start: 0.8157 (ptm) cc_final: 0.7694 (ptp) outliers start: 46 outliers final: 34 residues processed: 268 average time/residue: 0.1924 time to fit residues: 71.4615 Evaluate side-chains 261 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 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 C residue 200 SER Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 222 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 G residue 47 ASP Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 174 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 196 PHE Chi-restraints excluded: chain H residue 241 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: 0.8980 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 77 HIS E 206 ASN G 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.186485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.148036 restraints weight = 20510.212| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.60 r_work: 0.3618 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17971 Z= 0.119 Angle : 0.483 9.718 24383 Z= 0.267 Chirality : 0.040 0.257 2754 Planarity : 0.004 0.038 2913 Dihedral : 17.941 177.123 2857 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.23 % Allowed : 12.83 % Favored : 84.93 % 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: 1.91 (0.19), residues: 2040 helix: 2.20 (0.15), residues: 1200 sheet: -0.42 (0.46), residues: 128 loop : 0.04 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 258 TYR 0.010 0.001 TYR H 93 PHE 0.016 0.001 PHE B 125 TRP 0.014 0.001 TRP E 45 HIS 0.004 0.001 HIS E 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (17971) covalent geometry : angle 0.48257 / 0.27 (24383) hydrogen bonds : bond 0.04428 / 2.96 ( 828) hydrogen bonds : angle 4.02869 / 2.87 ( 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 277 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 237 time to evaluate : 0.683 Fit side-chains REVERT: A 210 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7289 (ptm) REVERT: A 213 GLN cc_start: 0.7424 (mt0) cc_final: 0.7170 (mt0) REVERT: A 262 LYS cc_start: 0.5443 (pttt) cc_final: 0.5055 (ptpt) REVERT: B 181 LYS cc_start: 0.8485 (pttp) cc_final: 0.8035 (ptpt) REVERT: B 182 ARG cc_start: 0.7321 (mtt90) cc_final: 0.7072 (mtm-85) REVERT: B 217 LYS cc_start: 0.7436 (mmtt) cc_final: 0.7034 (mmtp) REVERT: B 261 LYS cc_start: 0.7100 (mttm) cc_final: 0.6163 (mmmt) REVERT: B 269 GLN cc_start: 0.7472 (mm-40) cc_final: 0.7047 (mm-40) REVERT: C 85 ARG cc_start: 0.5877 (OUTLIER) cc_final: 0.5003 (mmt180) REVERT: C 188 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7944 (mm-30) REVERT: C 261 LYS cc_start: 0.5971 (mmtp) cc_final: 0.5527 (mmmt) REVERT: D 74 ARG cc_start: 0.7847 (ttp-170) cc_final: 0.7603 (ptm160) REVERT: D 188 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7752 (mm-30) REVERT: D 223 ASN cc_start: 0.6823 (p0) cc_final: 0.6491 (p0) REVERT: E 188 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7951 (mm-30) REVERT: F 188 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8200 (mm-30) REVERT: F 196 PHE cc_start: 0.9289 (OUTLIER) cc_final: 0.8427 (t80) REVERT: G 81 GLN cc_start: 0.6009 (mt0) cc_final: 0.5678 (mt0) REVERT: G 140 MET cc_start: 0.8772 (ttm) cc_final: 0.8467 (ttm) REVERT: G 188 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8208 (mm-30) REVERT: G 256 LEU cc_start: 0.8266 (mt) cc_final: 0.7989 (mp) REVERT: H 140 MET cc_start: 0.8863 (ttm) cc_final: 0.8203 (ttm) REVERT: H 210 MET cc_start: 0.8121 (ptm) cc_final: 0.7654 (ptp) REVERT: H 246 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6415 (mt-10) outliers start: 40 outliers final: 31 residues processed: 263 average time/residue: 0.1981 time to fit residues: 72.0502 Evaluate side-chains 254 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 210 MET 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 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 222 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 264 ASP Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 174 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 196 PHE Chi-restraints excluded: chain H residue 200 SER 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: 5.9990 chunk 110 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 193 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 165 optimal weight: 0.2980 chunk 173 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS D 77 HIS G 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.186844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.148774 restraints weight = 20733.842| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.54 r_work: 0.3616 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17971 Z= 0.115 Angle : 0.476 9.248 24383 Z= 0.262 Chirality : 0.040 0.257 2754 Planarity : 0.004 0.050 2913 Dihedral : 17.866 174.712 2857 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.01 % Allowed : 12.95 % Favored : 85.04 % 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: 1.98 (0.19), residues: 2040 helix: 2.24 (0.15), residues: 1200 sheet: -0.33 (0.47), residues: 128 loop : 0.07 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 249 TYR 0.009 0.001 TYR G 275 PHE 0.015 0.001 PHE B 125 TRP 0.014 0.001 TRP E 45 HIS 0.004 0.001 HIS E 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (17971) covalent geometry : angle 0.47578 / 0.26 (24383) hydrogen bonds : bond 0.04189 / 2.81 ( 828) hydrogen bonds : angle 3.97677 / 2.83 ( 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 272 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 0.699 Fit side-chains REVERT: A 107 LYS cc_start: 0.8565 (tttm) cc_final: 0.8140 (ttpp) REVERT: A 209 GLU cc_start: 0.7283 (tp30) cc_final: 0.6720 (tp30) REVERT: A 210 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7310 (ptm) REVERT: A 262 LYS cc_start: 0.5550 (pttt) cc_final: 0.5133 (ptpt) REVERT: B 181 LYS cc_start: 0.8401 (pttp) cc_final: 0.7889 (ptpt) REVERT: B 182 ARG cc_start: 0.7318 (mtt90) cc_final: 0.7058 (mtm-85) REVERT: B 217 LYS cc_start: 0.7384 (mmtt) cc_final: 0.7040 (mmtp) REVERT: B 261 LYS cc_start: 0.7172 (mttm) cc_final: 0.6255 (mmmt) REVERT: B 269 GLN cc_start: 0.7472 (mm-40) cc_final: 0.7017 (mm-40) REVERT: C 85 ARG cc_start: 0.6051 (OUTLIER) cc_final: 0.5149 (mmt180) REVERT: C 188 GLU cc_start: 0.8444 (mm-30) cc_final: 0.7943 (mm-30) REVERT: C 261 LYS cc_start: 0.5973 (mmtp) cc_final: 0.5534 (mmmt) REVERT: D 74 ARG cc_start: 0.7965 (ttp-170) cc_final: 0.7619 (ptm160) REVERT: D 188 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7821 (mm-30) REVERT: D 223 ASN cc_start: 0.6887 (p0) cc_final: 0.6646 (p0) REVERT: E 188 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7957 (mm-30) REVERT: F 47 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8134 (t0) REVERT: F 188 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8202 (mm-30) REVERT: F 196 PHE cc_start: 0.9323 (OUTLIER) cc_final: 0.8485 (t80) REVERT: G 81 GLN cc_start: 0.6001 (mt0) cc_final: 0.5681 (mt0) REVERT: G 140 MET cc_start: 0.8800 (ttm) cc_final: 0.8432 (ttm) REVERT: G 188 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8249 (mm-30) REVERT: G 256 LEU cc_start: 0.8258 (mt) cc_final: 0.8017 (mp) REVERT: H 140 MET cc_start: 0.8840 (ttm) cc_final: 0.8161 (ttm) REVERT: H 210 MET cc_start: 0.8140 (ptm) cc_final: 0.7841 (ptm) REVERT: H 246 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6459 (mt-10) outliers start: 36 outliers final: 31 residues processed: 256 average time/residue: 0.1877 time to fit residues: 66.8767 Evaluate side-chains 254 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 219 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 210 MET 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 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 117 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 222 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 47 ASP Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 174 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 196 PHE Chi-restraints excluded: chain H residue 241 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: 0.9980 chunk 201 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 170 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 156 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 223 ASN D 77 HIS G 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.186051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.147266 restraints weight = 20615.178| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.71 r_work: 0.3606 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17971 Z= 0.124 Angle : 0.492 8.776 24383 Z= 0.270 Chirality : 0.041 0.261 2754 Planarity : 0.004 0.040 2913 Dihedral : 17.837 174.715 2857 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.18 % Allowed : 13.39 % Favored : 84.43 % 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: 1.99 (0.19), residues: 2040 helix: 2.27 (0.15), residues: 1200 sheet: -0.36 (0.47), residues: 128 loop : 0.05 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 249 TYR 0.009 0.001 TYR H 93 PHE 0.014 0.002 PHE E 125 TRP 0.013 0.001 TRP E 45 HIS 0.005 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (17971) covalent geometry : angle 0.49213 / 0.27 (24383) hydrogen bonds : bond 0.04300 / 2.89 ( 828) hydrogen bonds : angle 3.98818 / 2.83 ( 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 264 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 0.733 Fit side-chains REVERT: A 107 LYS cc_start: 0.8557 (tttm) cc_final: 0.8138 (ttpp) REVERT: A 210 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7333 (ptm) REVERT: A 262 LYS cc_start: 0.5606 (pttt) cc_final: 0.5246 (ptpt) REVERT: B 181 LYS cc_start: 0.8431 (pttp) cc_final: 0.7920 (ptpt) REVERT: B 182 ARG cc_start: 0.7329 (mtt90) cc_final: 0.7083 (mtm-85) REVERT: B 217 LYS cc_start: 0.7319 (mmtt) cc_final: 0.6998 (mmtp) REVERT: B 269 GLN cc_start: 0.7497 (mm-40) cc_final: 0.7043 (mm-40) REVERT: C 85 ARG cc_start: 0.6072 (OUTLIER) cc_final: 0.5240 (mmt180) REVERT: C 188 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7936 (mm-30) REVERT: C 261 LYS cc_start: 0.6010 (mmtp) cc_final: 0.5583 (mmmt) REVERT: D 74 ARG cc_start: 0.7981 (ttp-170) cc_final: 0.7622 (ptm160) REVERT: D 188 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7868 (mm-30) REVERT: D 223 ASN cc_start: 0.6906 (p0) cc_final: 0.6666 (p0) REVERT: E 188 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7963 (mm-30) REVERT: F 188 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8235 (mm-30) REVERT: F 196 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.8452 (t80) REVERT: F 202 GLU cc_start: 0.6736 (pm20) cc_final: 0.6329 (pm20) REVERT: G 81 GLN cc_start: 0.6111 (mt0) cc_final: 0.5705 (mt0) REVERT: G 140 MET cc_start: 0.8813 (ttm) cc_final: 0.8439 (ttm) REVERT: G 188 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8249 (mm-30) REVERT: G 256 LEU cc_start: 0.8276 (mt) cc_final: 0.8024 (mp) REVERT: H 140 MET cc_start: 0.8868 (ttm) cc_final: 0.8212 (ttm) REVERT: H 210 MET cc_start: 0.8131 (ptm) cc_final: 0.7846 (ptm) REVERT: H 246 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6525 (mt-10) outliers start: 39 outliers final: 32 residues processed: 248 average time/residue: 0.1952 time to fit residues: 66.6623 Evaluate side-chains 254 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 219 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 210 MET 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 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 C residue 223 ASN Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 222 SER 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 116 ARG Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 55 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 142 optimal weight: 5.9990 chunk 202 optimal weight: 30.0000 chunk 89 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN G 77 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.182659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143696 restraints weight = 20751.826| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.60 r_work: 0.3554 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17971 Z= 0.195 Angle : 0.575 8.869 24383 Z= 0.310 Chirality : 0.044 0.279 2754 Planarity : 0.005 0.063 2913 Dihedral : 17.918 174.534 2857 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.23 % Allowed : 13.34 % Favored : 84.43 % 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: 1.71 (0.19), residues: 2040 helix: 2.13 (0.15), residues: 1200 sheet: -0.72 (0.45), residues: 128 loop : -0.18 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 249 TYR 0.013 0.002 TYR H 93 PHE 0.015 0.002 PHE E 125 TRP 0.012 0.002 TRP G 45 HIS 0.008 0.002 HIS D 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.19 (17971) covalent geometry : angle 0.57470 / 0.31 (24383) hydrogen bonds : bond 0.05281 / 3.59 ( 828) hydrogen bonds : angle 4.13805 / 2.94 ( 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 258 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 218 time to evaluate : 0.703 Fit side-chains REVERT: A 210 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7332 (ptm) REVERT: B 76 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7509 (mtp180) REVERT: B 181 LYS cc_start: 0.8548 (pttp) cc_final: 0.8069 (ptpt) REVERT: B 182 ARG cc_start: 0.7439 (mtt90) cc_final: 0.7212 (mtm-85) REVERT: B 196 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8535 (m-80) REVERT: B 217 LYS cc_start: 0.7220 (mmtt) cc_final: 0.6948 (mmtp) REVERT: B 269 GLN cc_start: 0.7515 (mm-40) cc_final: 0.7044 (mm-40) REVERT: C 85 ARG cc_start: 0.5841 (OUTLIER) cc_final: 0.5066 (mmt180) REVERT: C 188 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8074 (mm-30) REVERT: C 261 LYS cc_start: 0.6049 (mmtp) cc_final: 0.5609 (mmmt) REVERT: D 119 LYS cc_start: 0.7651 (tttm) cc_final: 0.7446 (ttpp) REVERT: D 188 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7894 (mm-30) REVERT: D 223 ASN cc_start: 0.6782 (p0) cc_final: 0.6470 (p0) REVERT: E 188 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8171 (mm-30) REVERT: F 188 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8243 (mm-30) REVERT: F 196 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8394 (t80) REVERT: F 202 GLU cc_start: 0.6955 (pm20) cc_final: 0.6740 (pm20) REVERT: F 238 GLU cc_start: 0.8186 (mp0) cc_final: 0.7842 (mp0) REVERT: F 260 LEU cc_start: 0.7643 (mp) cc_final: 0.7317 (mp) REVERT: G 81 GLN cc_start: 0.6122 (mt0) cc_final: 0.5703 (mt0) REVERT: G 140 MET cc_start: 0.8866 (ttm) cc_final: 0.8483 (ttm) REVERT: G 256 LEU cc_start: 0.8271 (mt) cc_final: 0.8021 (mp) REVERT: H 140 MET cc_start: 0.8820 (ttm) cc_final: 0.8240 (ttm) REVERT: H 210 MET cc_start: 0.8143 (ptm) cc_final: 0.7897 (ptm) REVERT: H 246 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6662 (mt-10) outliers start: 40 outliers final: 31 residues processed: 245 average time/residue: 0.1886 time to fit residues: 63.5915 Evaluate side-chains 248 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 210 MET 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 196 PHE 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 C residue 229 MET Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 171 VAL 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 F residue 116 ARG Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 124 ASP 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: 3.9990 chunk 104 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.0170 chunk 171 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 165 optimal weight: 0.0470 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 77 HIS G 77 HIS H 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.186100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.147459 restraints weight = 20651.208| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.68 r_work: 0.3607 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17971 Z= 0.109 Angle : 0.482 7.708 24383 Z= 0.266 Chirality : 0.040 0.259 2754 Planarity : 0.004 0.037 2913 Dihedral : 17.790 175.553 2857 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.01 % Allowed : 13.56 % Favored : 84.43 % 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: 1.89 (0.19), residues: 2040 helix: 2.27 (0.15), residues: 1200 sheet: -0.39 (0.35), residues: 208 loop : -0.12 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 258 TYR 0.008 0.001 TYR H 93 PHE 0.015 0.001 PHE B 125 TRP 0.014 0.001 TRP E 45 HIS 0.003 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (17971) covalent geometry : angle 0.48197 / 0.27 (24383) hydrogen bonds : bond 0.04126 / 2.76 ( 828) hydrogen bonds : angle 3.97563 / 2.82 ( 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 269 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 0.691 Fit side-chains REVERT: A 210 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7289 (ptm) REVERT: A 262 LYS cc_start: 0.5665 (pttt) cc_final: 0.5265 (ptpt) REVERT: B 181 LYS cc_start: 0.8422 (pttp) cc_final: 0.7909 (ptpt) REVERT: B 182 ARG cc_start: 0.7326 (mtt90) cc_final: 0.7094 (mtm-85) REVERT: B 196 PHE cc_start: 0.9272 (OUTLIER) cc_final: 0.8476 (m-80) REVERT: B 217 LYS cc_start: 0.7311 (mmtt) cc_final: 0.7063 (mmtp) REVERT: B 269 GLN cc_start: 0.7496 (mm-40) cc_final: 0.7030 (mm-40) REVERT: C 85 ARG cc_start: 0.6096 (OUTLIER) cc_final: 0.4740 (mmt180) REVERT: C 188 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8047 (mm-30) REVERT: C 261 LYS cc_start: 0.6054 (mmtp) cc_final: 0.5557 (mmmt) REVERT: D 188 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7870 (mm-30) REVERT: D 223 ASN cc_start: 0.6998 (p0) cc_final: 0.6781 (p0) REVERT: E 75 TYR cc_start: 0.7363 (m-10) cc_final: 0.7029 (m-10) REVERT: E 188 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8022 (mm-30) REVERT: F 188 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8248 (mm-30) REVERT: F 196 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8467 (t80) REVERT: F 202 GLU cc_start: 0.6890 (pm20) cc_final: 0.6644 (pm20) REVERT: F 238 GLU cc_start: 0.8126 (mp0) cc_final: 0.7767 (mp0) REVERT: F 260 LEU cc_start: 0.7628 (mp) cc_final: 0.7299 (mp) REVERT: G 81 GLN cc_start: 0.6106 (mt0) cc_final: 0.5694 (mt0) REVERT: G 140 MET cc_start: 0.8810 (ttm) cc_final: 0.8459 (ttm) REVERT: G 227 LYS cc_start: 0.7344 (ttpt) cc_final: 0.6756 (mmtm) REVERT: G 256 LEU cc_start: 0.8268 (mt) cc_final: 0.7994 (mp) REVERT: H 140 MET cc_start: 0.8803 (ttm) cc_final: 0.8294 (ttm) REVERT: H 210 MET cc_start: 0.8155 (ptm) cc_final: 0.7881 (ptm) REVERT: H 246 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6419 (mt-10) outliers start: 36 outliers final: 30 residues processed: 255 average time/residue: 0.1772 time to fit residues: 62.1287 Evaluate side-chains 256 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 210 MET 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 196 PHE 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 117 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 171 VAL 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 F residue 116 ARG Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 55 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: 0.6980 chunk 65 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 200 optimal weight: 30.0000 chunk 25 optimal weight: 9.9990 chunk 152 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN C 223 ASN D 77 HIS G 77 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.186237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147635 restraints weight = 20806.231| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.69 r_work: 0.3610 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4480 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= 0.114 Angle : 0.482 8.078 24383 Z= 0.265 Chirality : 0.040 0.261 2754 Planarity : 0.004 0.042 2913 Dihedral : 17.735 175.109 2857 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.01 % Allowed : 14.01 % Favored : 83.98 % 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: -0.26 (0.35), residues: 208 loop : -0.23 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 76 TYR 0.008 0.001 TYR H 93 PHE 0.015 0.001 PHE E 125 TRP 0.015 0.001 TRP E 45 HIS 0.006 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (17971) covalent geometry : angle 0.48246 / 0.26 (24383) hydrogen bonds : bond 0.04051 / 2.73 ( 828) hydrogen bonds : angle 3.95650 / 2.80 ( 2458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5030.61 seconds wall clock time: 86 minutes 51.87 seconds (5211.87 seconds total)