Starting phenix.real_space_refine on Sat Sep 12 18:37:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m99_23720/09_2026/7m99_23720.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m99_23720/09_2026/7m99_23720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m99_23720/09_2026/7m99_23720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m99_23720/09_2026/7m99_23720.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m99_23720/09_2026/7m99_23720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m99_23720/09_2026/7m99_23720.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7m99_23720/09_2026/7m99_23720.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m99_23720/09_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-2.2.1-6174/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: 3.99, per 1000 atoms: 0.23 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: 1.50 Conformation dependent library (CDL) restraints added in 707.3 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: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 36 through 53 Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 101 through 113 removed outlier: 3.858A pdb=" N PHE A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 134 removed outlier: 4.658A pdb=" N ASP A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 164 Processing helix chain 'A' and resid 174 through 181 removed outlier: 4.120A pdb=" N ALA A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 190 removed outlier: 3.609A pdb=" N ARG A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.522A pdb=" N LYS A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 238 removed outlier: 4.483A pdb=" N ILE A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 257 Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'B' and resid 20 through 29 Processing helix chain 'B' and resid 36 through 53 Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 101 through 113 removed outlier: 3.858A pdb=" N PHE B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 134 removed outlier: 4.007A pdb=" N ASP B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG B 128 " --> pdb=" O ASP B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 153 through 164 Processing helix chain 'B' and resid 175 through 181 Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 201 through 216 removed outlier: 3.522A pdb=" N LYS B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 238 removed outlier: 4.483A pdb=" N ILE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 257 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'C' and resid 20 through 29 Processing helix chain 'C' and resid 36 through 53 Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 101 through 113 removed outlier: 3.856A pdb=" N PHE C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 134 removed outlier: 3.598A pdb=" N ASP C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'C' and resid 174 through 181 removed outlier: 4.126A pdb=" N ALA C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 removed outlier: 3.511A pdb=" N ARG C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 removed outlier: 3.522A pdb=" N LYS C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 238 removed outlier: 4.345A pdb=" N ILE C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 257 Processing helix chain 'C' and resid 264 through 273 Processing helix chain 'D' and resid 20 through 29 Processing helix chain 'D' and resid 36 through 53 Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.857A pdb=" N PHE D 106 " --> pdb=" O PRO D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 134 Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 174 through 181 removed outlier: 4.110A pdb=" N ALA D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 190 removed outlier: 3.510A pdb=" N ARG D 189 " --> pdb=" O GLN D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 215 removed outlier: 3.522A pdb=" N LYS D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 238 removed outlier: 4.484A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 257 Processing helix chain 'D' and resid 264 through 273 Processing helix chain 'E' and resid 20 through 29 Processing helix chain 'E' and resid 36 through 53 Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 101 through 113 removed outlier: 3.857A pdb=" N PHE E 106 " --> pdb=" O PRO E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 134 removed outlier: 4.658A pdb=" N ASP E 127 " --> pdb=" O SER E 123 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG E 128 " --> pdb=" O ASP E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 174 through 181 removed outlier: 4.081A pdb=" N ALA E 178 " --> pdb=" O ASP E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 190 Processing helix chain 'E' and resid 201 through 215 removed outlier: 3.522A pdb=" N LYS E 205 " --> pdb=" O GLY E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 238 removed outlier: 4.488A pdb=" N ILE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 257 Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'F' and resid 20 through 29 Processing helix chain 'F' and resid 36 through 53 Processing helix chain 'F' and resid 65 through 77 Processing helix chain 'F' and resid 101 through 113 removed outlier: 3.857A pdb=" N PHE F 106 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 134 removed outlier: 3.599A pdb=" N ASP F 127 " --> pdb=" O SER F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 152 No H-bonds generated for 'chain 'F' and resid 150 through 152' Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 174 through 181 removed outlier: 4.110A pdb=" N ALA F 178 " --> pdb=" O ASP F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 190 removed outlier: 3.601A pdb=" N ARG F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 215 removed outlier: 3.522A pdb=" N LYS F 205 " --> pdb=" O GLY F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 238 removed outlier: 4.487A pdb=" N ILE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 257 Processing helix chain 'F' and resid 264 through 273 Processing helix chain 'G' and resid 20 through 29 Processing helix chain 'G' and resid 36 through 53 removed outlier: 3.817A pdb=" N GLY G 48 " --> pdb=" O ASP G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 101 through 113 removed outlier: 3.857A pdb=" N PHE G 106 " --> pdb=" O PRO G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 134 removed outlier: 4.657A pdb=" N ASP G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG G 128 " --> pdb=" O ASP G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 153 through 164 Processing helix chain 'G' and resid 174 through 181 removed outlier: 4.091A pdb=" N ALA G 178 " --> pdb=" O ASP G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 190 removed outlier: 3.533A pdb=" N ARG G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 215 removed outlier: 3.522A pdb=" N LYS G 205 " --> pdb=" O GLY G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 238 removed outlier: 4.489A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 257 Processing helix chain 'G' and resid 264 through 273 Processing helix chain 'H' and resid 20 through 29 Processing helix chain 'H' and resid 36 through 53 Processing helix chain 'H' and resid 65 through 77 Processing helix chain 'H' and resid 101 through 113 removed outlier: 3.857A pdb=" N PHE H 106 " --> pdb=" O PRO H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 134 removed outlier: 4.657A pdb=" N ASP H 127 " --> pdb=" O SER H 123 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG H 128 " --> pdb=" O ASP H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 152 No H-bonds generated for 'chain 'H' and resid 150 through 152' Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 174 through 181 removed outlier: 4.118A pdb=" N ALA H 178 " --> pdb=" O ASP H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 removed outlier: 3.527A pdb=" N ARG H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 215 removed outlier: 3.521A pdb=" N LYS H 205 " --> pdb=" O GLY H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 238 removed outlier: 4.482A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 257 Processing helix chain 'H' and resid 264 through 273 Processing sheet with id=AA1, first strand: chain 'A' and resid 171 through 173 removed outlier: 5.842A pdb=" N VAL A 58 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 94 removed outlier: 6.650A pdb=" N VAL A 92 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 173 removed outlier: 5.905A pdb=" N VAL B 58 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 94 removed outlier: 6.651A pdb=" N VAL B 92 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 171 through 172 removed outlier: 5.858A pdb=" N VAL C 58 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG C 57 " --> pdb=" O LEU C 194 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.651A pdb=" N VAL C 92 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 171 through 172 removed outlier: 5.963A pdb=" N VAL D 58 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 91 through 94 removed outlier: 7.051A pdb=" N VAL D 92 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 171 through 172 removed outlier: 6.002A pdb=" N VAL E 58 " --> pdb=" O GLY E 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.650A pdb=" N VAL E 92 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 171 through 172 removed outlier: 6.283A pdb=" N VAL F 58 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 91 through 94 removed outlier: 6.650A pdb=" N VAL F 92 " --> pdb=" O ILE F 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 171 through 172 removed outlier: 6.124A pdb=" N VAL G 58 " --> pdb=" O GLY G 172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 91 through 94 removed outlier: 6.651A pdb=" N VAL G 92 " --> pdb=" O ILE G 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 171 through 172 removed outlier: 5.963A pdb=" N VAL H 58 " --> pdb=" O GLY H 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 91 through 94 removed outlier: 6.637A pdb=" N VAL H 92 " --> pdb=" O ILE H 142 " (cutoff:3.500A) 802 hydrogen bonds defined for protein. 2406 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 2.04 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: 20166 2.11 - 4.22: 3874 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 17.730 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.740 ------------------------------------------------------------------------------- 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 : 1.538 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 1.53752 / 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 : 0.712 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: 0.2167 time to fit residues: 143.7920 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 : 0.692 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.192156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.155807 restraints weight = 21083.254| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.46 r_work: 0.3685 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17971 Z= 0.167 Angle : 0.610 10.462 24383 Z= 0.336 Chirality : 0.043 0.257 2754 Planarity : 0.006 0.077 2913 Dihedral : 18.233 177.431 2871 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.34 % Allowed : 8.82 % Favored : 88.84 % 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: 1.03 (0.18), residues: 2040 helix: 1.16 (0.14), residues: 1192 sheet: -0.00 (0.51), residues: 96 loop : 0.17 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 76 TYR 0.015 0.001 TYR H 93 PHE 0.022 0.002 PHE B 125 TRP 0.014 0.002 TRP G 211 HIS 0.004 0.001 HIS C 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (17971) covalent geometry : angle 0.60976 / 0.34 (24383) hydrogen bonds : bond 0.06402 / 4.25 ( 828) hydrogen bonds : angle 4.79191 / 3.44 ( 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: 42 poor density : 285 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7156 (ttpp) cc_final: 0.6940 (ttpp) REVERT: A 184 GLU cc_start: 0.8275 (tt0) cc_final: 0.7761 (pt0) REVERT: A 213 GLN cc_start: 0.7772 (mt0) cc_final: 0.7288 (mt0) REVERT: B 129 THR cc_start: 0.8414 (m) cc_final: 0.8172 (m) REVERT: B 181 LYS cc_start: 0.8639 (pttp) cc_final: 0.8387 (mttt) REVERT: B 217 LYS cc_start: 0.7080 (mmtt) cc_final: 0.6387 (mmtp) REVERT: B 261 LYS cc_start: 0.6891 (mttm) cc_final: 0.5892 (mmmt) REVERT: C 76 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.6336 (ttp-170) REVERT: C 188 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7957 (mm-30) REVERT: C 203 ASP cc_start: 0.7979 (m-30) cc_final: 0.7412 (t0) REVERT: D 188 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7805 (mm-30) REVERT: D 265 LYS cc_start: 0.7011 (ttmm) cc_final: 0.6793 (ttmt) REVERT: E 181 LYS cc_start: 0.8130 (mttt) cc_final: 0.7910 (mtpp) REVERT: E 188 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8034 (mm-30) REVERT: E 222 SER cc_start: 0.7454 (m) cc_final: 0.7222 (m) REVERT: F 188 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8169 (mm-30) REVERT: G 81 GLN cc_start: 0.6081 (mt0) cc_final: 0.5701 (mt0) REVERT: G 140 MET cc_start: 0.8642 (ttm) cc_final: 0.8131 (ttm) REVERT: G 188 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8165 (mm-30) REVERT: G 246 GLU cc_start: 0.6665 (mt-10) cc_final: 0.6431 (mt-10) REVERT: G 256 LEU cc_start: 0.8456 (mt) cc_final: 0.8225 (mp) REVERT: H 140 MET cc_start: 0.8626 (ttm) cc_final: 0.7951 (ttm) REVERT: H 148 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7717 (ptt180) outliers start: 42 outliers final: 24 residues processed: 320 average time/residue: 0.1914 time to fit residues: 82.6940 Evaluate side-chains 264 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 124 ASP Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 225 LYS Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 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: 0.8980 chunk 145 optimal weight: 0.1980 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: 0.9980 chunk 144 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN B 269 GLN C 213 GLN E 81 GLN E 98 GLN E 206 ASN E 213 GLN F 206 ASN G 77 HIS H 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.191387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.152521 restraints weight = 20929.135| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.69 r_work: 0.3682 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17971 Z= 0.123 Angle : 0.506 9.351 24383 Z= 0.280 Chirality : 0.041 0.266 2754 Planarity : 0.004 0.046 2913 Dihedral : 18.136 178.418 2859 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.95 % Allowed : 10.10 % Favored : 87.95 % 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 (0.18), residues: 2040 helix: 1.80 (0.15), residues: 1200 sheet: 0.02 (0.53), residues: 96 loop : 0.31 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 182 TYR 0.012 0.001 TYR D 75 PHE 0.018 0.002 PHE B 125 TRP 0.016 0.001 TRP G 45 HIS 0.003 0.001 HIS E 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (17971) covalent geometry : angle 0.50556 / 0.28 (24383) hydrogen bonds : bond 0.05081 / 3.38 ( 828) hydrogen bonds : angle 4.30587 / 3.08 ( 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 311 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 184 GLU cc_start: 0.8244 (tt0) cc_final: 0.7976 (pt0) REVERT: B 85 ARG cc_start: 0.6135 (mtt180) cc_final: 0.5625 (mtt180) REVERT: B 182 ARG cc_start: 0.7981 (mpt180) cc_final: 0.7137 (mtt90) REVERT: B 217 LYS cc_start: 0.7224 (mmtt) cc_final: 0.6658 (mmtp) REVERT: B 261 LYS cc_start: 0.6934 (mttm) cc_final: 0.5917 (mmmt) REVERT: C 188 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7884 (mm-30) REVERT: C 203 ASP cc_start: 0.8074 (m-30) cc_final: 0.7471 (t0) REVERT: D 75 TYR cc_start: 0.7529 (m-80) cc_final: 0.7257 (m-80) REVERT: D 188 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7832 (mm-30) REVERT: D 265 LYS cc_start: 0.7131 (ttmm) cc_final: 0.6905 (mtpt) REVERT: E 181 LYS cc_start: 0.8069 (mttt) cc_final: 0.7825 (mtpp) REVERT: E 188 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7905 (mm-30) REVERT: F 163 ASP cc_start: 0.8325 (m-30) cc_final: 0.8117 (m-30) REVERT: F 188 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7999 (mm-30) REVERT: F 196 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8332 (t80) REVERT: G 81 GLN cc_start: 0.6121 (mt0) cc_final: 0.5739 (mt0) REVERT: G 131 GLU cc_start: 0.7884 (tt0) cc_final: 0.7616 (mt-10) REVERT: G 140 MET cc_start: 0.8687 (ttm) cc_final: 0.8402 (ttm) REVERT: G 188 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8227 (mm-30) REVERT: G 231 ARG cc_start: 0.7312 (ttp80) cc_final: 0.6788 (ptt90) REVERT: G 256 LEU cc_start: 0.8284 (mt) cc_final: 0.8018 (mp) REVERT: H 140 MET cc_start: 0.8738 (ttm) cc_final: 0.8058 (ttm) REVERT: H 210 MET cc_start: 0.7950 (ptm) cc_final: 0.7733 (ptm) REVERT: H 243 ARG cc_start: 0.7931 (mtt-85) cc_final: 0.7662 (mtt-85) outliers start: 35 outliers final: 24 residues processed: 301 average time/residue: 0.1820 time to fit residues: 74.8260 Evaluate side-chains 269 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP 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 181 LYS Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 255 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 0.0370 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 191 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 overall best weight: 1.1460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 269 GLN C 269 GLN E 81 GLN E 98 GLN E 206 ASN E 213 GLN G 37 GLN G 77 HIS H 37 GLN H 206 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.187622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.148783 restraints weight = 20735.587| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.67 r_work: 0.3621 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3605 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= 0.142 Angle : 0.522 9.593 24383 Z= 0.285 Chirality : 0.042 0.275 2754 Planarity : 0.005 0.039 2913 Dihedral : 18.071 174.623 2857 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.06 % Allowed : 11.83 % 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: 1.90 (0.18), residues: 2040 helix: 2.07 (0.15), residues: 1200 sheet: -0.11 (0.53), residues: 96 loop : 0.17 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 182 TYR 0.014 0.001 TYR H 93 PHE 0.019 0.002 PHE G 125 TRP 0.013 0.001 TRP G 45 HIS 0.006 0.001 HIS E 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (17971) covalent geometry : angle 0.52194 / 0.29 (24383) hydrogen bonds : bond 0.04979 / 3.34 ( 828) hydrogen bonds : angle 4.13184 / 2.96 ( 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 290 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 253 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 170 LEU cc_start: 0.8640 (mt) cc_final: 0.8408 (mp) REVERT: A 184 GLU cc_start: 0.8329 (tt0) cc_final: 0.7979 (pt0) REVERT: B 76 ARG cc_start: 0.7521 (ttm170) cc_final: 0.7286 (mtp180) REVERT: B 217 LYS cc_start: 0.7311 (mmtt) cc_final: 0.6801 (mmtp) REVERT: B 261 LYS cc_start: 0.7004 (mttm) cc_final: 0.6028 (mmmt) REVERT: C 188 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7966 (mm-30) REVERT: D 188 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7769 (mm-30) REVERT: E 188 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8001 (mm-30) REVERT: F 47 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8132 (t0) REVERT: F 188 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8188 (mm-30) REVERT: G 81 GLN cc_start: 0.5933 (mt0) cc_final: 0.5587 (mt0) REVERT: G 140 MET cc_start: 0.8758 (ttm) cc_final: 0.8398 (ttm) REVERT: G 188 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8242 (mm-30) REVERT: G 231 ARG cc_start: 0.7508 (ttp80) cc_final: 0.6972 (ptt90) REVERT: G 256 LEU cc_start: 0.8316 (mt) cc_final: 0.8062 (mp) REVERT: H 75 TYR cc_start: 0.6933 (m-80) cc_final: 0.6509 (m-80) REVERT: H 140 MET cc_start: 0.8777 (ttm) cc_final: 0.8163 (ttm) REVERT: H 210 MET cc_start: 0.8175 (ptm) cc_final: 0.7856 (ptm) outliers start: 37 outliers final: 28 residues processed: 278 average time/residue: 0.1808 time to fit residues: 69.0186 Evaluate side-chains 256 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 227 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 124 ASP 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 222 SER Chi-restraints excluded: chain B residue 226 SER 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 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 F residue 47 ASP Chi-restraints excluded: chain F residue 264 ASP Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 196 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 166 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 198 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS B 269 GLN C 213 GLN C 269 GLN E 206 ASN G 77 HIS H 206 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.185144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.145276 restraints weight = 20644.939| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.78 r_work: 0.3577 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17971 Z= 0.162 Angle : 0.534 9.353 24383 Z= 0.292 Chirality : 0.043 0.283 2754 Planarity : 0.005 0.040 2913 Dihedral : 18.030 174.503 2857 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.23 % Allowed : 12.28 % Favored : 85.49 % 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: 1.81 (0.19), residues: 2040 helix: 2.09 (0.15), residues: 1200 sheet: -0.33 (0.52), residues: 96 loop : -0.00 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 50 TYR 0.011 0.001 TYR H 93 PHE 0.016 0.002 PHE F 125 TRP 0.014 0.002 TRP G 45 HIS 0.007 0.002 HIS E 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (17971) covalent geometry : angle 0.53449 / 0.29 (24383) hydrogen bonds : bond 0.05165 / 3.48 ( 828) hydrogen bonds : angle 4.12870 / 2.95 ( 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 273 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 0.571 Fit side-chains REVERT: A 76 ARG cc_start: 0.7489 (ttm170) cc_final: 0.7126 (mtp180) REVERT: A 170 LEU cc_start: 0.8655 (mt) cc_final: 0.8434 (mp) REVERT: A 184 GLU cc_start: 0.8471 (tt0) cc_final: 0.8042 (pt0) REVERT: A 262 LYS cc_start: 0.5450 (pttt) cc_final: 0.4992 (ptpt) REVERT: B 217 LYS cc_start: 0.7440 (mmtt) cc_final: 0.7018 (mmtp) REVERT: B 261 LYS cc_start: 0.7050 (mttm) cc_final: 0.6151 (mmmt) REVERT: C 188 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8004 (mm-30) REVERT: D 188 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7888 (mm-30) REVERT: D 202 GLU cc_start: 0.6643 (pm20) cc_final: 0.6440 (pt0) REVERT: E 188 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8053 (mm-30) REVERT: F 188 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8237 (mm-30) REVERT: F 196 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.8462 (t80) REVERT: G 81 GLN cc_start: 0.5932 (mt0) cc_final: 0.5586 (mt0) REVERT: G 188 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8289 (mm-30) REVERT: G 256 LEU cc_start: 0.8323 (mt) cc_final: 0.8050 (mp) REVERT: G 275 TYR cc_start: 0.7912 (m-80) cc_final: 0.7552 (m-80) REVERT: H 140 MET cc_start: 0.8884 (ttm) cc_final: 0.8270 (ttm) REVERT: H 210 MET cc_start: 0.8144 (ptm) cc_final: 0.7679 (ptp) outliers start: 40 outliers final: 28 residues processed: 261 average time/residue: 0.1884 time to fit residues: 67.7327 Evaluate side-chains 249 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 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 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 194 LEU Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 150 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 213 GLN G 77 HIS H 206 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.187000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147987 restraints weight = 20517.631| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.71 r_work: 0.3617 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17971 Z= 0.116 Angle : 0.476 8.438 24383 Z= 0.263 Chirality : 0.041 0.276 2754 Planarity : 0.004 0.037 2913 Dihedral : 17.938 177.622 2857 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.01 % Allowed : 12.56 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.19), residues: 2040 helix: 2.23 (0.15), residues: 1200 sheet: -0.24 (0.54), residues: 96 loop : 0.05 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 258 TYR 0.011 0.001 TYR H 93 PHE 0.015 0.002 PHE B 125 TRP 0.014 0.001 TRP G 45 HIS 0.004 0.001 HIS E 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (17971) covalent geometry : angle 0.47553 / 0.26 (24383) hydrogen bonds : bond 0.04363 / 2.92 ( 828) hydrogen bonds : angle 4.01476 / 2.86 ( 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 270 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 0.746 Fit side-chains REVERT: A 107 LYS cc_start: 0.8548 (tttm) cc_final: 0.8126 (ttpp) REVERT: A 170 LEU cc_start: 0.8508 (mt) cc_final: 0.8299 (mp) REVERT: A 184 GLU cc_start: 0.8426 (tt0) cc_final: 0.7975 (pt0) REVERT: A 262 LYS cc_start: 0.5468 (pttt) cc_final: 0.5066 (ptpt) REVERT: B 182 ARG cc_start: 0.7675 (mmt180) cc_final: 0.7302 (mtt180) REVERT: B 217 LYS cc_start: 0.7409 (mmtt) cc_final: 0.7033 (mmtp) REVERT: B 261 LYS cc_start: 0.7105 (mttm) cc_final: 0.6176 (mmmt) REVERT: B 269 GLN cc_start: 0.7472 (mm-40) cc_final: 0.7040 (mm-40) REVERT: C 85 ARG cc_start: 0.5890 (OUTLIER) cc_final: 0.4899 (mmt180) REVERT: C 188 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7969 (mm-30) REVERT: C 210 MET cc_start: 0.8087 (ttm) cc_final: 0.7841 (ptp) REVERT: C 261 LYS cc_start: 0.5971 (mmtp) cc_final: 0.5516 (mmmt) REVERT: D 188 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7812 (mm-30) REVERT: E 188 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7990 (mm-30) REVERT: F 188 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8218 (mm-30) REVERT: F 196 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8479 (t80) REVERT: G 81 GLN cc_start: 0.6006 (mt0) cc_final: 0.5627 (mt0) REVERT: G 140 MET cc_start: 0.8770 (ttm) cc_final: 0.8488 (ttm) REVERT: G 188 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8240 (mm-30) REVERT: G 256 LEU cc_start: 0.8312 (mt) cc_final: 0.8039 (mp) REVERT: H 75 TYR cc_start: 0.6977 (m-80) cc_final: 0.6548 (m-80) REVERT: H 140 MET cc_start: 0.8835 (ttm) cc_final: 0.8170 (ttm) REVERT: H 210 MET cc_start: 0.8116 (ptm) cc_final: 0.7680 (ptp) outliers start: 36 outliers final: 31 residues processed: 256 average time/residue: 0.1844 time to fit residues: 65.8067 Evaluate side-chains 255 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 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 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 117 VAL 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 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 222 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 174 ASP Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 71 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 165 optimal weight: 0.4980 chunk 173 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 HIS C 213 GLN G 77 HIS H 206 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.187206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.148291 restraints weight = 20702.381| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.62 r_work: 0.3624 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4132 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= 0.113 Angle : 0.472 7.407 24383 Z= 0.260 Chirality : 0.040 0.276 2754 Planarity : 0.004 0.037 2913 Dihedral : 17.891 178.834 2857 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.18 % Allowed : 13.00 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.19), residues: 2040 helix: 2.27 (0.15), residues: 1200 sheet: 0.47 (0.57), residues: 88 loop : 0.02 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 258 TYR 0.009 0.001 TYR H 93 PHE 0.015 0.001 PHE B 125 TRP 0.013 0.001 TRP E 45 HIS 0.004 0.001 HIS E 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (17971) covalent geometry : angle 0.47220 / 0.26 (24383) hydrogen bonds : bond 0.04146 / 2.78 ( 828) hydrogen bonds : angle 3.97598 / 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 280 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 0.709 Fit side-chains REVERT: A 107 LYS cc_start: 0.8555 (tttm) cc_final: 0.8138 (ttpp) REVERT: A 170 LEU cc_start: 0.8457 (mt) cc_final: 0.8228 (mp) REVERT: A 262 LYS cc_start: 0.5492 (pttt) cc_final: 0.5082 (ptpt) REVERT: B 182 ARG cc_start: 0.7667 (mmt180) cc_final: 0.7298 (mtt180) REVERT: B 217 LYS cc_start: 0.7378 (mmtt) cc_final: 0.6912 (mmtp) REVERT: C 85 ARG cc_start: 0.6063 (OUTLIER) cc_final: 0.4972 (mmt180) REVERT: C 188 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7939 (mm-30) REVERT: C 261 LYS cc_start: 0.5989 (mmtp) cc_final: 0.5613 (mmmt) REVERT: D 85 ARG cc_start: 0.5574 (mtt180) cc_final: 0.5197 (mmm160) REVERT: D 188 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7820 (mm-30) REVERT: E 188 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7973 (mm-30) REVERT: F 47 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8172 (t0) REVERT: F 116 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8377 (mmt-90) REVERT: F 119 LYS cc_start: 0.8083 (ttmm) cc_final: 0.7872 (tppt) REVERT: F 188 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8245 (mm-30) REVERT: F 196 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.8448 (t80) REVERT: F 202 GLU cc_start: 0.6771 (pm20) cc_final: 0.6455 (pm20) REVERT: G 81 GLN cc_start: 0.6103 (mt0) cc_final: 0.5703 (mt0) REVERT: G 140 MET cc_start: 0.8793 (ttm) cc_final: 0.8432 (ttm) REVERT: G 188 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8260 (mm-30) REVERT: G 256 LEU cc_start: 0.8323 (mt) cc_final: 0.8058 (mp) REVERT: H 140 MET cc_start: 0.8824 (ttm) cc_final: 0.8147 (ttm) REVERT: H 210 MET cc_start: 0.8128 (ptm) cc_final: 0.7690 (ptp) REVERT: H 246 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6450 (mt-10) outliers start: 39 outliers final: 33 residues processed: 266 average time/residue: 0.1841 time to fit residues: 68.2627 Evaluate side-chains 260 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 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 221 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 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 F residue 224 LEU 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 174 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain H residue 122 VAL 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: 0.5980 chunk 201 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 170 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 137 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 156 optimal weight: 0.0050 chunk 35 optimal weight: 0.1980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 HIS C 213 GLN E 213 GLN G 77 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.188312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.149822 restraints weight = 20597.966| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.68 r_work: 0.3637 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17971 Z= 0.103 Angle : 0.460 7.384 24383 Z= 0.254 Chirality : 0.040 0.273 2754 Planarity : 0.004 0.036 2913 Dihedral : 17.825 175.327 2857 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.90 % Allowed : 13.23 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.19), residues: 2040 helix: 2.32 (0.15), residues: 1200 sheet: 0.62 (0.59), residues: 88 loop : 0.08 (0.22), residues: 752 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 0.004 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (17971) covalent geometry : angle 0.46023 / 0.25 (24383) hydrogen bonds : bond 0.03835 / 2.57 ( 828) hydrogen bonds : angle 3.92470 / 2.79 ( 2458) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 236 time to evaluate : 0.675 Fit side-chains REVERT: A 107 LYS cc_start: 0.8558 (tttm) cc_final: 0.8139 (ttpp) REVERT: A 213 GLN cc_start: 0.7348 (mt0) cc_final: 0.7097 (mt0) REVERT: A 262 LYS cc_start: 0.5579 (pttt) cc_final: 0.5198 (ptpt) REVERT: B 182 ARG cc_start: 0.7633 (mmt180) cc_final: 0.7275 (mtt180) REVERT: B 269 GLN cc_start: 0.7688 (mm-40) cc_final: 0.6934 (mm-40) REVERT: C 85 ARG cc_start: 0.6109 (OUTLIER) cc_final: 0.4622 (mmt180) REVERT: C 188 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7902 (mm-30) REVERT: C 261 LYS cc_start: 0.5995 (mmtp) cc_final: 0.5629 (mmmt) REVERT: D 85 ARG cc_start: 0.5554 (mtt180) cc_final: 0.5202 (mmm160) REVERT: D 188 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7822 (mm-30) REVERT: E 188 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7959 (mm-30) REVERT: F 47 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8181 (t0) REVERT: F 116 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8232 (mmt-90) REVERT: F 119 LYS cc_start: 0.8066 (ttmm) cc_final: 0.7827 (tppt) REVERT: F 188 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8242 (mm-30) REVERT: F 196 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8454 (t80) REVERT: G 81 GLN cc_start: 0.6136 (mt0) cc_final: 0.5746 (mt0) REVERT: G 140 MET cc_start: 0.8803 (ttm) cc_final: 0.8445 (ttm) REVERT: G 188 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8277 (mm-30) REVERT: G 231 ARG cc_start: 0.7415 (ttp80) cc_final: 0.7004 (ptt90) REVERT: G 256 LEU cc_start: 0.8305 (mt) cc_final: 0.8039 (mp) REVERT: H 140 MET cc_start: 0.8832 (ttm) cc_final: 0.8171 (ttm) REVERT: H 210 MET cc_start: 0.8088 (ptm) cc_final: 0.7826 (ptm) REVERT: H 246 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6480 (mt-10) outliers start: 34 outliers final: 28 residues processed: 256 average time/residue: 0.1869 time to fit residues: 66.2725 Evaluate side-chains 255 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 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 255 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 122 VAL 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: 4.9990 chunk 202 optimal weight: 30.0000 chunk 89 optimal weight: 2.9990 chunk 111 optimal weight: 0.1980 chunk 197 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 121 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 HIS G 77 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.185735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.147405 restraints weight = 20703.013| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.59 r_work: 0.3611 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17971 Z= 0.136 Angle : 0.505 7.871 24383 Z= 0.275 Chirality : 0.041 0.282 2754 Planarity : 0.004 0.036 2913 Dihedral : 17.844 174.889 2857 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.06 % Allowed : 13.34 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.19), residues: 2040 helix: 2.32 (0.15), residues: 1200 sheet: -0.28 (0.48), residues: 128 loop : 0.07 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 258 TYR 0.011 0.001 TYR H 93 PHE 0.014 0.002 PHE B 125 TRP 0.012 0.001 TRP G 45 HIS 0.005 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (17971) covalent geometry : angle 0.50518 / 0.27 (24383) hydrogen bonds : bond 0.04383 / 2.96 ( 828) hydrogen bonds : angle 3.98539 / 2.83 ( 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 260 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 0.591 Fit side-chains REVERT: A 107 LYS cc_start: 0.8551 (tttm) cc_final: 0.8121 (ttpp) REVERT: A 262 LYS cc_start: 0.5664 (pttt) cc_final: 0.5280 (ptpt) REVERT: B 182 ARG cc_start: 0.7666 (mmt180) cc_final: 0.7315 (mtt180) REVERT: B 217 LYS cc_start: 0.7453 (mmmt) cc_final: 0.6889 (mmtp) REVERT: B 269 GLN cc_start: 0.7505 (mm-40) cc_final: 0.6856 (mm-40) REVERT: C 85 ARG cc_start: 0.5964 (OUTLIER) cc_final: 0.5243 (mmt180) REVERT: C 188 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7924 (mm-30) REVERT: C 246 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6601 (mt-10) REVERT: C 261 LYS cc_start: 0.6014 (mmtp) cc_final: 0.5666 (mmmt) REVERT: D 85 ARG cc_start: 0.5834 (mtt180) cc_final: 0.5386 (mmm160) REVERT: D 119 LYS cc_start: 0.7550 (tttm) cc_final: 0.7335 (ttpp) REVERT: D 188 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7867 (mm-30) REVERT: D 258 ARG cc_start: 0.7344 (mtt90) cc_final: 0.7133 (mtp85) REVERT: E 188 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7973 (mm-30) REVERT: F 116 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8288 (mmt-90) REVERT: F 119 LYS cc_start: 0.8033 (ttmm) cc_final: 0.7793 (tppt) REVERT: F 188 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8254 (mm-30) REVERT: F 196 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8309 (t80) REVERT: G 81 GLN cc_start: 0.6133 (mt0) cc_final: 0.5737 (mt0) REVERT: G 140 MET cc_start: 0.8845 (ttm) cc_final: 0.8466 (ttm) REVERT: G 188 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8234 (mm-30) REVERT: G 256 LEU cc_start: 0.8293 (mt) cc_final: 0.8026 (mp) REVERT: H 140 MET cc_start: 0.8842 (ttm) cc_final: 0.8180 (ttm) REVERT: H 210 MET cc_start: 0.8084 (ptm) cc_final: 0.7782 (ptm) REVERT: H 246 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6506 (mt-10) outliers start: 37 outliers final: 29 residues processed: 245 average time/residue: 0.1766 time to fit residues: 60.2054 Evaluate side-chains 249 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 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 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 116 ARG Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 122 VAL 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: 4.9990 chunk 104 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 171 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 HIS C 269 GLN G 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.181081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.141683 restraints weight = 20683.787| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.61 r_work: 0.3540 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17971 Z= 0.230 Angle : 0.628 7.939 24383 Z= 0.336 Chirality : 0.047 0.302 2754 Planarity : 0.006 0.080 2913 Dihedral : 17.951 174.928 2857 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.95 % Allowed : 13.45 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.19), residues: 2040 helix: 1.99 (0.15), residues: 1200 sheet: -0.80 (0.33), residues: 216 loop : -0.29 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 74 TYR 0.015 0.002 TYR H 93 PHE 0.022 0.002 PHE C 125 TRP 0.013 0.002 TRP F 20 HIS 0.008 0.002 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.23 (17971) covalent geometry : angle 0.62758 / 0.34 (24383) hydrogen bonds : bond 0.05991 / 4.09 ( 828) hydrogen bonds : angle 4.26665 / 3.04 ( 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 256 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 0.671 Fit side-chains REVERT: A 213 GLN cc_start: 0.7516 (mt0) cc_final: 0.7290 (mt0) REVERT: B 182 ARG cc_start: 0.7880 (mmt180) cc_final: 0.7538 (mtt180) REVERT: B 229 MET cc_start: 0.6174 (mtt) cc_final: 0.5793 (mtt) REVERT: B 269 GLN cc_start: 0.7575 (mm-40) cc_final: 0.6949 (mm-40) REVERT: C 85 ARG cc_start: 0.5812 (OUTLIER) cc_final: 0.5280 (mmt180) REVERT: C 188 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8053 (mm-30) REVERT: C 261 LYS cc_start: 0.6101 (mmtp) cc_final: 0.5612 (mmmt) REVERT: E 188 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8163 (mm-30) REVERT: E 261 LYS cc_start: 0.6544 (mmtm) cc_final: 0.6327 (mmtm) REVERT: F 116 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8308 (mmt-90) REVERT: F 188 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8337 (mm-30) REVERT: F 196 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8311 (t80) REVERT: F 260 LEU cc_start: 0.7670 (mp) cc_final: 0.7382 (mp) REVERT: G 81 GLN cc_start: 0.5978 (mt0) cc_final: 0.5514 (mt0) REVERT: G 124 ASP cc_start: 0.8339 (m-30) cc_final: 0.7949 (m-30) REVERT: G 140 MET cc_start: 0.8887 (ttm) cc_final: 0.8539 (ttm) REVERT: G 223 ASN cc_start: 0.5899 (t0) cc_final: 0.5483 (t0) REVERT: G 256 LEU cc_start: 0.8277 (mt) cc_final: 0.8027 (mp) REVERT: H 75 TYR cc_start: 0.7507 (m-10) cc_final: 0.6916 (m-80) REVERT: H 140 MET cc_start: 0.8809 (ttm) cc_final: 0.8332 (ttm) REVERT: H 210 MET cc_start: 0.8142 (ptm) cc_final: 0.7731 (ptp) REVERT: H 246 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6747 (mt-10) outliers start: 35 outliers final: 25 residues processed: 248 average time/residue: 0.1906 time to fit residues: 65.0445 Evaluate side-chains 237 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 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 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 F residue 224 LEU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 122 VAL 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: 4.9990 chunk 76 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 200 optimal weight: 30.0000 chunk 25 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 HIS ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 GLN G 77 HIS G 213 GLN H 77 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.183698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.145353 restraints weight = 20781.257| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.56 r_work: 0.3566 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17971 Z= 0.146 Angle : 0.532 8.033 24383 Z= 0.290 Chirality : 0.042 0.291 2754 Planarity : 0.004 0.039 2913 Dihedral : 17.843 176.408 2857 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.56 % Allowed : 14.17 % Favored : 84.26 % 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: 1.66 (0.19), residues: 2040 helix: 2.14 (0.15), residues: 1200 sheet: -0.52 (0.34), residues: 208 loop : -0.30 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 258 TYR 0.011 0.001 TYR H 93 PHE 0.018 0.002 PHE C 125 TRP 0.014 0.002 TRP G 45 HIS 0.007 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (17971) covalent geometry : angle 0.53188 / 0.29 (24383) hydrogen bonds : bond 0.04826 / 3.26 ( 828) hydrogen bonds : angle 4.08151 / 2.90 ( 2458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4835.27 seconds wall clock time: 83 minutes 24.88 seconds (5004.88 seconds total)