Starting phenix.real_space_refine on Wed Jan 14 15:36:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8djb_27459/01_2026/8djb_27459.cif Found real_map, /net/cci-nas-00/data/ceres_data/8djb_27459/01_2026/8djb_27459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8djb_27459/01_2026/8djb_27459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8djb_27459/01_2026/8djb_27459.map" model { file = "/net/cci-nas-00/data/ceres_data/8djb_27459/01_2026/8djb_27459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8djb_27459/01_2026/8djb_27459.cif" } resolution = 3.18 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 1 8.98 5 S 68 5.16 5 C 10576 2.51 5 N 2896 2.21 5 O 3240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16781 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2470 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "B" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, E, G, D, F, H Time building chain proxies: 3.39, per 1000 atoms: 0.20 Number of scatterers: 16781 At special positions: 0 Unit cell: (144.039, 144.039, 119.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 1 19.00 S 68 16.00 O 3240 8.00 N 2896 7.00 C 10576 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: 1.56 Conformation dependent library (CDL) restraints added in 688.7 milliseconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 16 sheets defined 51.6% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 21 through 39 removed outlier: 3.731A pdb=" N GLY A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 58 removed outlier: 3.584A pdb=" N TYR A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 107 removed outlier: 4.174A pdb=" N MET A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.690A pdb=" N ARG A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.668A pdb=" N LYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 202 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 247 through 257 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'B' and resid 124 through 130 Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.690A pdb=" N ARG B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.668A pdb=" N LYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 230 through 242 Processing helix chain 'B' and resid 247 through 257 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 284 through 290 Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'D' and resid 124 through 130 Processing helix chain 'D' and resid 145 through 156 removed outlier: 3.689A pdb=" N ARG D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 173 removed outlier: 3.668A pdb=" N LYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA D 173 " --> pdb=" O ASP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 230 through 242 Processing helix chain 'D' and resid 247 through 257 Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'D' and resid 284 through 290 Processing helix chain 'D' and resid 323 through 334 Processing helix chain 'F' and resid 124 through 130 Processing helix chain 'F' and resid 145 through 156 removed outlier: 3.689A pdb=" N ARG F 149 " --> pdb=" O ASP F 145 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS F 150 " --> pdb=" O GLU F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 173 removed outlier: 3.668A pdb=" N LYS F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 216 through 224 Processing helix chain 'F' and resid 230 through 242 Processing helix chain 'F' and resid 247 through 257 Processing helix chain 'F' and resid 279 through 284 Processing helix chain 'F' and resid 284 through 290 Processing helix chain 'F' and resid 323 through 334 Processing helix chain 'H' and resid 124 through 130 Processing helix chain 'H' and resid 145 through 156 removed outlier: 3.690A pdb=" N ARG H 149 " --> pdb=" O ASP H 145 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS H 150 " --> pdb=" O GLU H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 173 removed outlier: 3.668A pdb=" N LYS H 172 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 Processing helix chain 'H' and resid 213 through 215 No H-bonds generated for 'chain 'H' and resid 213 through 215' Processing helix chain 'H' and resid 216 through 224 Processing helix chain 'H' and resid 230 through 242 Processing helix chain 'H' and resid 247 through 257 Processing helix chain 'H' and resid 279 through 284 Processing helix chain 'H' and resid 284 through 290 Processing helix chain 'H' and resid 323 through 334 Processing helix chain 'G' and resid 21 through 39 removed outlier: 3.731A pdb=" N GLY G 37 " --> pdb=" O TYR G 33 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS G 39 " --> pdb=" O THR G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 58 removed outlier: 3.584A pdb=" N TYR G 51 " --> pdb=" O THR G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 107 removed outlier: 4.175A pdb=" N MET G 107 " --> pdb=" O GLN G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 130 Processing helix chain 'G' and resid 145 through 156 removed outlier: 3.690A pdb=" N ARG G 149 " --> pdb=" O ASP G 145 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 173 removed outlier: 3.668A pdb=" N LYS G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 202 Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 216 through 224 Processing helix chain 'G' and resid 230 through 242 Processing helix chain 'G' and resid 247 through 257 Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 284 through 290 Processing helix chain 'G' and resid 323 through 334 Processing helix chain 'C' and resid 21 through 39 removed outlier: 3.730A pdb=" N GLY C 37 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 58 removed outlier: 3.584A pdb=" N TYR C 51 " --> pdb=" O THR C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 107 removed outlier: 4.174A pdb=" N MET C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 130 Processing helix chain 'C' and resid 145 through 156 removed outlier: 3.690A pdb=" N ARG C 149 " --> pdb=" O ASP C 145 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.667A pdb=" N LYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 230 through 242 Processing helix chain 'C' and resid 247 through 257 Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 290 Processing helix chain 'C' and resid 323 through 334 Processing helix chain 'E' and resid 21 through 39 removed outlier: 3.731A pdb=" N GLY E 37 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS E 39 " --> pdb=" O THR E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 58 removed outlier: 3.584A pdb=" N TYR E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 107 removed outlier: 4.175A pdb=" N MET E 107 " --> pdb=" O GLN E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 130 Processing helix chain 'E' and resid 145 through 156 removed outlier: 3.690A pdb=" N ARG E 149 " --> pdb=" O ASP E 145 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.667A pdb=" N LYS E 172 " --> pdb=" O SER E 168 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 202 Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 224 Processing helix chain 'E' and resid 230 through 242 Processing helix chain 'E' and resid 247 through 257 Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 284 through 290 Processing helix chain 'E' and resid 323 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.363A pdb=" N ILE A 317 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL A 296 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU A 319 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 161 Processing sheet with id=AA4, first strand: chain 'B' and resid 263 through 268 removed outlier: 6.363A pdb=" N ILE B 317 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL B 296 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU B 319 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AA6, first strand: chain 'D' and resid 263 through 268 removed outlier: 6.364A pdb=" N ILE D 317 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL D 296 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU D 319 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AA8, first strand: chain 'F' and resid 263 through 268 removed outlier: 6.364A pdb=" N ILE F 317 " --> pdb=" O VAL F 296 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL F 296 " --> pdb=" O ILE F 317 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU F 319 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 158 through 161 Processing sheet with id=AB1, first strand: chain 'H' and resid 263 through 268 removed outlier: 6.364A pdb=" N ILE H 317 " --> pdb=" O VAL H 296 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL H 296 " --> pdb=" O ILE H 317 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU H 319 " --> pdb=" O ILE H 294 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 158 through 161 Processing sheet with id=AB3, first strand: chain 'G' and resid 263 through 268 removed outlier: 6.363A pdb=" N ILE G 317 " --> pdb=" O VAL G 296 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL G 296 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU G 319 " --> pdb=" O ILE G 294 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AB5, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.364A pdb=" N ILE C 317 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL C 296 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU C 319 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AB7, first strand: chain 'E' and resid 263 through 268 removed outlier: 6.364A pdb=" N ILE E 317 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL E 296 " --> pdb=" O ILE E 317 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU E 319 " --> pdb=" O ILE E 294 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2580 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2948 1.31 - 1.43: 4018 1.43 - 1.56: 9942 1.56 - 1.68: 0 1.68 - 1.81: 112 Bond restraints: 17020 Sorted by residual: bond pdb=" C ILE E 229 " pdb=" O ILE E 229 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.02e-02 9.61e+03 2.83e+01 bond pdb=" C ILE H 229 " pdb=" O ILE H 229 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.02e-02 9.61e+03 2.79e+01 bond pdb=" C ILE B 229 " pdb=" O ILE B 229 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.02e-02 9.61e+03 2.79e+01 bond pdb=" C ILE A 229 " pdb=" O ILE A 229 " ideal model delta sigma weight residual 1.236 1.183 0.053 1.02e-02 9.61e+03 2.75e+01 bond pdb=" C ILE G 229 " pdb=" O ILE G 229 " ideal model delta sigma weight residual 1.236 1.183 0.053 1.02e-02 9.61e+03 2.74e+01 ... (remaining 17015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 22080 1.63 - 3.26: 815 3.26 - 4.90: 109 4.90 - 6.53: 8 6.53 - 8.16: 12 Bond angle restraints: 23024 Sorted by residual: angle pdb=" N TYR G 74 " pdb=" CA TYR G 74 " pdb=" C TYR G 74 " ideal model delta sigma weight residual 111.14 105.33 5.81 1.08e+00 8.57e-01 2.89e+01 angle pdb=" N TYR C 74 " pdb=" CA TYR C 74 " pdb=" C TYR C 74 " ideal model delta sigma weight residual 111.14 105.34 5.80 1.08e+00 8.57e-01 2.88e+01 angle pdb=" N TYR A 74 " pdb=" CA TYR A 74 " pdb=" C TYR A 74 " ideal model delta sigma weight residual 111.14 105.34 5.80 1.08e+00 8.57e-01 2.88e+01 angle pdb=" N TYR E 74 " pdb=" CA TYR E 74 " pdb=" C TYR E 74 " ideal model delta sigma weight residual 111.14 105.35 5.79 1.08e+00 8.57e-01 2.87e+01 angle pdb=" C ARG E 313 " pdb=" CA ARG E 313 " pdb=" CB ARG E 313 " ideal model delta sigma weight residual 114.41 106.34 8.07 2.30e+00 1.89e-01 1.23e+01 ... (remaining 23019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 9652 17.79 - 35.58: 484 35.58 - 53.36: 136 53.36 - 71.15: 68 71.15 - 88.94: 4 Dihedral angle restraints: 10344 sinusoidal: 4192 harmonic: 6152 Sorted by residual: dihedral pdb=" CG ARG B 116 " pdb=" CD ARG B 116 " pdb=" NE ARG B 116 " pdb=" CZ ARG B 116 " ideal model delta sinusoidal sigma weight residual -90.00 -28.08 -61.92 2 1.50e+01 4.44e-03 1.66e+01 dihedral pdb=" CG ARG C 116 " pdb=" CD ARG C 116 " pdb=" NE ARG C 116 " pdb=" CZ ARG C 116 " ideal model delta sinusoidal sigma weight residual -90.00 -28.12 -61.88 2 1.50e+01 4.44e-03 1.66e+01 dihedral pdb=" CG ARG H 116 " pdb=" CD ARG H 116 " pdb=" NE ARG H 116 " pdb=" CZ ARG H 116 " ideal model delta sinusoidal sigma weight residual -90.00 -28.12 -61.88 2 1.50e+01 4.44e-03 1.66e+01 ... (remaining 10341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2374 0.077 - 0.155: 276 0.155 - 0.232: 26 0.232 - 0.310: 8 0.310 - 0.387: 8 Chirality restraints: 2692 Sorted by residual: chirality pdb=" CA GLU H 144 " pdb=" N GLU H 144 " pdb=" C GLU H 144 " pdb=" CB GLU H 144 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA GLU D 144 " pdb=" N GLU D 144 " pdb=" C GLU D 144 " pdb=" CB GLU D 144 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CA GLU A 144 " pdb=" N GLU A 144 " pdb=" C GLU A 144 " pdb=" CB GLU A 144 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 2689 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 240 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C SER B 240 " -0.037 2.00e-02 2.50e+03 pdb=" O SER B 240 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG B 241 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 240 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C SER F 240 " 0.037 2.00e-02 2.50e+03 pdb=" O SER F 240 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG F 241 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 240 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C SER H 240 " -0.037 2.00e-02 2.50e+03 pdb=" O SER H 240 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG H 241 " 0.012 2.00e-02 2.50e+03 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.55: 68 2.55 - 3.20: 15006 3.20 - 3.85: 30223 3.85 - 4.49: 42350 4.49 - 5.14: 71893 Nonbonded interactions: 159540 Sorted by model distance: nonbonded pdb=" CB ARG C 135 " pdb=" OE2 GLU C 138 " model vdw 1.908 3.440 nonbonded pdb=" CB ARG G 135 " pdb=" OE2 GLU G 138 " model vdw 1.909 3.440 nonbonded pdb=" CB ARG E 135 " pdb=" OE2 GLU E 138 " model vdw 1.909 3.440 nonbonded pdb=" CB ARG F 135 " pdb=" OE2 GLU F 138 " model vdw 1.909 3.440 nonbonded pdb=" CB ARG B 135 " pdb=" OE2 GLU B 138 " model vdw 1.909 3.440 ... (remaining 159535 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 'C' and resid 20 through 336) selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 2.160 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.890 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 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 : 0.005 0.054 17020 Z= 0.372 Angle : 0.724 8.161 23024 Z= 0.471 Chirality : 0.055 0.387 2692 Planarity : 0.004 0.021 2988 Dihedral : 12.904 88.941 6392 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.21 % Favored : 95.61 % Rotamer: Outliers : 6.96 % Allowed : 6.52 % Favored : 86.52 % 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: -0.69 (0.18), residues: 2140 helix: 0.21 (0.16), residues: 1036 sheet: 0.55 (0.33), residues: 304 loop : -1.69 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 329 TYR 0.025 0.002 TYR E 51 PHE 0.006 0.001 PHE C 87 TRP 0.006 0.001 TRP G 52 HIS 0.002 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00540 (17020) covalent geometry : angle 0.72434 (23024) hydrogen bonds : bond 0.20132 ( 892) hydrogen bonds : angle 7.25013 ( 2580) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 466 time to evaluate : 0.661 Fit side-chains REVERT: A 98 LEU cc_start: 0.8720 (tp) cc_final: 0.8506 (tp) REVERT: B 229 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7761 (mm) REVERT: B 310 TYR cc_start: 0.8797 (t80) cc_final: 0.8550 (t80) REVERT: D 229 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7690 (mm) REVERT: D 310 TYR cc_start: 0.8782 (t80) cc_final: 0.8528 (t80) REVERT: F 229 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7725 (mm) REVERT: F 310 TYR cc_start: 0.8778 (t80) cc_final: 0.8524 (t80) REVERT: H 170 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8352 (mp) REVERT: H 229 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7796 (mm) REVERT: H 310 TYR cc_start: 0.8828 (t80) cc_final: 0.8565 (t80) REVERT: G 38 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6297 (m-10) REVERT: G 76 THR cc_start: 0.8910 (m) cc_final: 0.8522 (m) REVERT: G 80 ILE cc_start: 0.9387 (mt) cc_final: 0.9171 (mt) REVERT: G 102 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7865 (mm-30) REVERT: C 80 ILE cc_start: 0.9395 (mt) cc_final: 0.9173 (mt) REVERT: E 38 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.6608 (m-10) outliers start: 128 outliers final: 26 residues processed: 570 average time/residue: 0.1823 time to fit residues: 142.0243 Evaluate side-chains 285 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 252 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 229 ILE Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 39 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 HIS ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 GLN C 39 HIS ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.116577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.079939 restraints weight = 27036.776| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.30 r_work: 0.2871 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17020 Z= 0.153 Angle : 0.642 12.808 23024 Z= 0.314 Chirality : 0.048 0.159 2692 Planarity : 0.004 0.030 2988 Dihedral : 5.710 59.740 2444 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.83 % Allowed : 13.75 % Favored : 83.42 % 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: -0.13 (0.18), residues: 2140 helix: 0.72 (0.16), residues: 1040 sheet: 0.28 (0.31), residues: 304 loop : -1.26 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 22 TYR 0.041 0.002 TYR C 74 PHE 0.026 0.002 PHE A 40 TRP 0.018 0.003 TRP A 52 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00356 (17020) covalent geometry : angle 0.64186 (23024) hydrogen bonds : bond 0.04056 ( 892) hydrogen bonds : angle 5.09836 ( 2580) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 270 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 74 TYR cc_start: 0.8454 (m-10) cc_final: 0.7966 (m-80) REVERT: A 104 MET cc_start: 0.8195 (tpp) cc_final: 0.7790 (ttp) REVERT: A 114 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7818 (mttt) REVERT: B 275 LEU cc_start: 0.8498 (mp) cc_final: 0.8182 (mp) REVERT: B 287 ASP cc_start: 0.8536 (m-30) cc_final: 0.8271 (m-30) REVERT: F 275 LEU cc_start: 0.8504 (mp) cc_final: 0.8170 (mp) REVERT: G 74 TYR cc_start: 0.8578 (m-80) cc_final: 0.8055 (m-80) REVERT: G 103 GLN cc_start: 0.8513 (tp-100) cc_final: 0.8287 (tm-30) REVERT: G 104 MET cc_start: 0.8170 (tpp) cc_final: 0.7796 (ttp) REVERT: G 107 MET cc_start: 0.8361 (ptp) cc_final: 0.8118 (ptt) REVERT: C 74 TYR cc_start: 0.8560 (m-80) cc_final: 0.8033 (m-80) REVERT: C 104 MET cc_start: 0.8167 (tpp) cc_final: 0.7722 (ttp) REVERT: E 74 TYR cc_start: 0.8528 (m-80) cc_final: 0.8057 (m-80) REVERT: E 82 LEU cc_start: 0.9315 (mm) cc_final: 0.9092 (mm) REVERT: E 104 MET cc_start: 0.8183 (tpp) cc_final: 0.7754 (ttp) REVERT: E 114 LYS cc_start: 0.7986 (mtpp) cc_final: 0.7785 (mttt) outliers start: 52 outliers final: 26 residues processed: 304 average time/residue: 0.1585 time to fit residues: 69.6705 Evaluate side-chains 252 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 71 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 19 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 86 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 ASN F 216 ASN H 216 ASN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.115631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.078705 restraints weight = 27486.493| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.55 r_work: 0.2817 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17020 Z= 0.128 Angle : 0.536 12.272 23024 Z= 0.269 Chirality : 0.046 0.131 2692 Planarity : 0.003 0.021 2988 Dihedral : 4.786 59.349 2402 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.90 % Allowed : 16.14 % Favored : 81.96 % 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: 0.36 (0.18), residues: 2140 helix: 1.25 (0.16), residues: 1040 sheet: 0.21 (0.29), residues: 304 loop : -1.08 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 313 TYR 0.021 0.001 TYR C 74 PHE 0.019 0.001 PHE A 75 TRP 0.008 0.001 TRP C 52 HIS 0.004 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00293 (17020) covalent geometry : angle 0.53612 (23024) hydrogen bonds : bond 0.03949 ( 892) hydrogen bonds : angle 4.74848 ( 2580) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 38 PHE cc_start: 0.6003 (OUTLIER) cc_final: 0.5598 (m-80) REVERT: A 74 TYR cc_start: 0.8538 (m-10) cc_final: 0.8032 (m-80) REVERT: A 104 MET cc_start: 0.8199 (tpp) cc_final: 0.7772 (ttp) REVERT: A 114 LYS cc_start: 0.8318 (mtpp) cc_final: 0.8086 (mmtt) REVERT: B 275 LEU cc_start: 0.8690 (mp) cc_final: 0.8333 (mp) REVERT: D 275 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8382 (mp) REVERT: F 332 ASN cc_start: 0.8755 (t0) cc_final: 0.8501 (m-40) REVERT: G 40 PHE cc_start: 0.7783 (t80) cc_final: 0.7384 (t80) REVERT: G 74 TYR cc_start: 0.8608 (m-80) cc_final: 0.8112 (m-80) REVERT: G 90 LEU cc_start: 0.8839 (tt) cc_final: 0.8634 (tp) REVERT: G 103 GLN cc_start: 0.8611 (tp-100) cc_final: 0.8409 (tp-100) REVERT: C 40 PHE cc_start: 0.7862 (t80) cc_final: 0.7526 (t80) REVERT: C 74 TYR cc_start: 0.8570 (m-80) cc_final: 0.8118 (m-80) REVERT: C 90 LEU cc_start: 0.8823 (tt) cc_final: 0.8622 (tp) REVERT: C 105 LYS cc_start: 0.8726 (tttt) cc_final: 0.8519 (tttm) REVERT: E 74 TYR cc_start: 0.8527 (m-80) cc_final: 0.8138 (m-80) REVERT: E 90 LEU cc_start: 0.8946 (tt) cc_final: 0.8698 (tp) REVERT: E 104 MET cc_start: 0.8237 (tpp) cc_final: 0.7926 (ttp) REVERT: E 105 LYS cc_start: 0.8731 (tttt) cc_final: 0.8497 (tttm) REVERT: E 114 LYS cc_start: 0.8326 (mtpp) cc_final: 0.8089 (mmtt) outliers start: 35 outliers final: 22 residues processed: 263 average time/residue: 0.1439 time to fit residues: 56.0306 Evaluate side-chains 251 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 95 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 204 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 199 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 117 optimal weight: 7.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.111538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.074655 restraints weight = 27802.761| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.27 r_work: 0.2758 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.6425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17020 Z= 0.185 Angle : 0.596 14.123 23024 Z= 0.297 Chirality : 0.047 0.133 2692 Planarity : 0.004 0.033 2988 Dihedral : 4.925 59.547 2394 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.93 % Allowed : 15.71 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.18), residues: 2140 helix: 1.26 (0.16), residues: 1012 sheet: 0.42 (0.29), residues: 304 loop : -1.08 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 213 TYR 0.016 0.002 TYR C 74 PHE 0.018 0.002 PHE A 40 TRP 0.016 0.001 TRP G 52 HIS 0.003 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00446 (17020) covalent geometry : angle 0.59640 (23024) hydrogen bonds : bond 0.04520 ( 892) hydrogen bonds : angle 4.79629 ( 2580) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 247 time to evaluate : 0.660 Fit side-chains REVERT: A 38 PHE cc_start: 0.6250 (OUTLIER) cc_final: 0.5704 (m-80) REVERT: B 300 ASP cc_start: 0.8613 (m-30) cc_final: 0.8342 (t0) REVERT: G 40 PHE cc_start: 0.7447 (t80) cc_final: 0.7185 (t80) REVERT: G 74 TYR cc_start: 0.8636 (m-80) cc_final: 0.8255 (m-80) REVERT: G 172 LYS cc_start: 0.8927 (mmtm) cc_final: 0.8684 (mmtp) REVERT: C 40 PHE cc_start: 0.7543 (t80) cc_final: 0.7282 (t80) REVERT: C 74 TYR cc_start: 0.8640 (m-80) cc_final: 0.8237 (m-80) REVERT: C 105 LYS cc_start: 0.9019 (tttt) cc_final: 0.8789 (tttm) REVERT: C 172 LYS cc_start: 0.8846 (mmtm) cc_final: 0.8591 (mmtp) REVERT: E 105 LYS cc_start: 0.8928 (tttt) cc_final: 0.8685 (tttm) outliers start: 54 outliers final: 31 residues processed: 286 average time/residue: 0.1486 time to fit residues: 62.3186 Evaluate side-chains 249 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 98 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 140 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 68 optimal weight: 0.0050 chunk 151 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 209 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.112257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.075247 restraints weight = 27518.100| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.30 r_work: 0.2771 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.6581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17020 Z= 0.134 Angle : 0.553 12.736 23024 Z= 0.267 Chirality : 0.046 0.175 2692 Planarity : 0.003 0.021 2988 Dihedral : 4.182 58.629 2386 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.07 % Allowed : 17.72 % Favored : 80.22 % 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: 0.57 (0.18), residues: 2140 helix: 1.44 (0.16), residues: 1012 sheet: 0.57 (0.29), residues: 304 loop : -1.03 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 313 TYR 0.021 0.001 TYR G 51 PHE 0.014 0.001 PHE A 40 TRP 0.010 0.001 TRP G 52 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00317 (17020) covalent geometry : angle 0.55278 (23024) hydrogen bonds : bond 0.03815 ( 892) hydrogen bonds : angle 4.64263 ( 2580) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 232 time to evaluate : 0.708 Fit side-chains REVERT: A 38 PHE cc_start: 0.6136 (OUTLIER) cc_final: 0.5609 (m-80) REVERT: A 40 PHE cc_start: 0.7580 (t80) cc_final: 0.7030 (t80) REVERT: A 54 PHE cc_start: 0.9065 (m-80) cc_final: 0.8818 (m-80) REVERT: A 74 TYR cc_start: 0.8571 (m-10) cc_final: 0.8039 (m-80) REVERT: B 300 ASP cc_start: 0.8628 (m-30) cc_final: 0.8400 (t0) REVERT: G 74 TYR cc_start: 0.8691 (m-80) cc_final: 0.8340 (m-80) REVERT: G 105 LYS cc_start: 0.8760 (tttm) cc_final: 0.8429 (ttmt) REVERT: G 172 LYS cc_start: 0.8851 (mmtm) cc_final: 0.8590 (mmtp) REVERT: C 40 PHE cc_start: 0.7517 (t80) cc_final: 0.7219 (t80) REVERT: C 74 TYR cc_start: 0.8630 (m-80) cc_final: 0.8306 (m-80) REVERT: C 105 LYS cc_start: 0.8849 (tttt) cc_final: 0.8642 (tttm) REVERT: E 105 LYS cc_start: 0.8838 (tttt) cc_final: 0.8631 (tttm) outliers start: 38 outliers final: 28 residues processed: 261 average time/residue: 0.1459 time to fit residues: 56.4321 Evaluate side-chains 252 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 186 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 97 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 121 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 chunk 210 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.109610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.073385 restraints weight = 27634.936| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.16 r_work: 0.2742 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.6870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 17020 Z= 0.223 Angle : 0.592 13.613 23024 Z= 0.290 Chirality : 0.047 0.170 2692 Planarity : 0.004 0.031 2988 Dihedral : 4.348 57.084 2386 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.50 % Allowed : 17.23 % Favored : 80.27 % 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: 0.52 (0.18), residues: 2140 helix: 1.32 (0.16), residues: 1016 sheet: 0.64 (0.28), residues: 304 loop : -1.00 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 308 TYR 0.023 0.002 TYR C 51 PHE 0.017 0.001 PHE E 40 TRP 0.009 0.001 TRP G 52 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00551 (17020) covalent geometry : angle 0.59163 (23024) hydrogen bonds : bond 0.04497 ( 892) hydrogen bonds : angle 4.80448 ( 2580) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 239 time to evaluate : 0.886 Fit side-chains REVERT: A 38 PHE cc_start: 0.6373 (OUTLIER) cc_final: 0.5743 (m-80) REVERT: A 40 PHE cc_start: 0.7630 (t80) cc_final: 0.7065 (t80) REVERT: A 74 TYR cc_start: 0.8585 (m-10) cc_final: 0.8131 (m-80) REVERT: G 74 TYR cc_start: 0.8730 (m-80) cc_final: 0.8294 (m-80) REVERT: G 105 LYS cc_start: 0.8889 (tttm) cc_final: 0.8601 (ttmt) REVERT: C 40 PHE cc_start: 0.7565 (t80) cc_final: 0.7262 (t80) REVERT: C 74 TYR cc_start: 0.8703 (m-80) cc_final: 0.8277 (m-80) REVERT: E 74 TYR cc_start: 0.8751 (m-80) cc_final: 0.8361 (m-80) REVERT: E 321 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.9211 (mt) outliers start: 46 outliers final: 28 residues processed: 271 average time/residue: 0.1445 time to fit residues: 58.0913 Evaluate side-chains 261 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 321 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 9 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 189 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 146 optimal weight: 0.0770 chunk 114 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 209 optimal weight: 0.0670 chunk 42 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.112256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.075707 restraints weight = 27259.952| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.27 r_work: 0.2785 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.6936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17020 Z= 0.104 Angle : 0.550 13.880 23024 Z= 0.262 Chirality : 0.045 0.180 2692 Planarity : 0.003 0.033 2988 Dihedral : 4.129 58.390 2386 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.85 % Allowed : 17.50 % Favored : 80.65 % 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: 0.71 (0.19), residues: 2140 helix: 1.55 (0.16), residues: 1012 sheet: 0.66 (0.29), residues: 304 loop : -0.98 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 308 TYR 0.022 0.001 TYR E 51 PHE 0.016 0.001 PHE E 40 TRP 0.011 0.001 TRP E 52 HIS 0.002 0.001 HIS F 286 Details of bonding type rmsd covalent geometry : bond 0.00229 (17020) covalent geometry : angle 0.55010 (23024) hydrogen bonds : bond 0.03374 ( 892) hydrogen bonds : angle 4.61370 ( 2580) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 0.670 Fit side-chains REVERT: A 38 PHE cc_start: 0.6178 (OUTLIER) cc_final: 0.5531 (m-80) REVERT: A 40 PHE cc_start: 0.7661 (t80) cc_final: 0.7096 (t80) REVERT: A 74 TYR cc_start: 0.8532 (m-10) cc_final: 0.8075 (m-80) REVERT: A 105 LYS cc_start: 0.8861 (tttp) cc_final: 0.8538 (ttmt) REVERT: B 200 LYS cc_start: 0.9013 (ttmm) cc_final: 0.8669 (ttpt) REVERT: D 200 LYS cc_start: 0.9015 (ttmm) cc_final: 0.8680 (ttpt) REVERT: H 200 LYS cc_start: 0.9014 (ttmm) cc_final: 0.8673 (ttpt) REVERT: G 74 TYR cc_start: 0.8695 (m-80) cc_final: 0.8248 (m-80) REVERT: G 105 LYS cc_start: 0.8801 (tttm) cc_final: 0.8551 (ttmt) REVERT: C 40 PHE cc_start: 0.7510 (t80) cc_final: 0.7185 (t80) REVERT: C 74 TYR cc_start: 0.8717 (m-80) cc_final: 0.8355 (m-80) REVERT: E 73 MET cc_start: 0.8186 (ptm) cc_final: 0.7944 (ptp) REVERT: E 74 TYR cc_start: 0.8769 (m-80) cc_final: 0.8357 (m-80) outliers start: 34 outliers final: 24 residues processed: 262 average time/residue: 0.1419 time to fit residues: 55.3276 Evaluate side-chains 254 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 215 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 88 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN H 332 ASN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.109513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.074203 restraints weight = 27689.070| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.34 r_work: 0.2740 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.7091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 17020 Z= 0.216 Angle : 0.600 14.181 23024 Z= 0.291 Chirality : 0.047 0.180 2692 Planarity : 0.004 0.033 2988 Dihedral : 4.289 58.130 2386 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.58 % Allowed : 18.21 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 2140 helix: 1.39 (0.16), residues: 1016 sheet: 0.66 (0.28), residues: 304 loop : -1.04 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 22 TYR 0.020 0.002 TYR C 51 PHE 0.015 0.001 PHE E 40 TRP 0.008 0.001 TRP E 52 HIS 0.003 0.001 HIS F 286 Details of bonding type rmsd covalent geometry : bond 0.00529 (17020) covalent geometry : angle 0.59982 (23024) hydrogen bonds : bond 0.04329 ( 892) hydrogen bonds : angle 4.78332 ( 2580) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 0.710 Fit side-chains REVERT: A 38 PHE cc_start: 0.6311 (OUTLIER) cc_final: 0.5643 (m-80) REVERT: A 40 PHE cc_start: 0.7645 (t80) cc_final: 0.7079 (t80) REVERT: A 74 TYR cc_start: 0.8522 (m-10) cc_final: 0.8071 (m-80) REVERT: A 105 LYS cc_start: 0.8911 (tttp) cc_final: 0.8601 (ttmt) REVERT: G 74 TYR cc_start: 0.8661 (m-80) cc_final: 0.8293 (m-80) REVERT: G 105 LYS cc_start: 0.8840 (tttm) cc_final: 0.8593 (ttmt) REVERT: C 40 PHE cc_start: 0.7573 (t80) cc_final: 0.7246 (t80) REVERT: C 74 TYR cc_start: 0.8769 (m-80) cc_final: 0.8404 (m-80) REVERT: E 103 GLN cc_start: 0.8644 (tp-100) cc_final: 0.8412 (tp40) outliers start: 29 outliers final: 22 residues processed: 261 average time/residue: 0.1400 time to fit residues: 54.4023 Evaluate side-chains 255 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 232 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 215 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 82 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 172 optimal weight: 0.2980 chunk 73 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 332 ASN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.110890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.076998 restraints weight = 27556.701| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.32 r_work: 0.2772 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.7133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17020 Z= 0.140 Angle : 0.579 13.773 23024 Z= 0.274 Chirality : 0.046 0.185 2692 Planarity : 0.003 0.035 2988 Dihedral : 4.212 59.973 2386 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.63 % Allowed : 18.59 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 2140 helix: 1.45 (0.16), residues: 1012 sheet: 0.70 (0.28), residues: 304 loop : -1.03 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 308 TYR 0.022 0.001 TYR C 51 PHE 0.014 0.001 PHE E 40 TRP 0.009 0.001 TRP E 52 HIS 0.002 0.001 HIS D 286 Details of bonding type rmsd covalent geometry : bond 0.00334 (17020) covalent geometry : angle 0.57947 (23024) hydrogen bonds : bond 0.03708 ( 892) hydrogen bonds : angle 4.71346 ( 2580) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.725 Fit side-chains REVERT: A 38 PHE cc_start: 0.6124 (OUTLIER) cc_final: 0.5497 (m-80) REVERT: A 40 PHE cc_start: 0.7592 (t80) cc_final: 0.7022 (t80) REVERT: A 74 TYR cc_start: 0.8536 (m-10) cc_final: 0.8102 (m-80) REVERT: A 105 LYS cc_start: 0.8863 (tttp) cc_final: 0.8568 (ttmt) REVERT: G 74 TYR cc_start: 0.8690 (m-80) cc_final: 0.8277 (m-80) REVERT: G 105 LYS cc_start: 0.8823 (tttm) cc_final: 0.8589 (ttmt) REVERT: C 40 PHE cc_start: 0.7501 (t80) cc_final: 0.7174 (t80) REVERT: C 74 TYR cc_start: 0.8794 (m-80) cc_final: 0.8402 (m-80) REVERT: E 74 TYR cc_start: 0.8809 (m-80) cc_final: 0.8390 (m-80) outliers start: 30 outliers final: 23 residues processed: 255 average time/residue: 0.1352 time to fit residues: 51.6479 Evaluate side-chains 249 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 215 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 37 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 137 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 332 ASN ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.111345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.075405 restraints weight = 27258.096| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.16 r_work: 0.2787 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.7210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17020 Z= 0.125 Angle : 0.576 14.478 23024 Z= 0.272 Chirality : 0.046 0.187 2692 Planarity : 0.003 0.033 2988 Dihedral : 4.135 58.449 2386 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.30 % Allowed : 19.13 % Favored : 79.57 % 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: 0.68 (0.18), residues: 2140 helix: 1.52 (0.16), residues: 1012 sheet: 0.75 (0.28), residues: 304 loop : -1.01 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 22 TYR 0.020 0.001 TYR C 51 PHE 0.013 0.001 PHE E 40 TRP 0.009 0.001 TRP E 52 HIS 0.002 0.001 HIS F 286 Details of bonding type rmsd covalent geometry : bond 0.00292 (17020) covalent geometry : angle 0.57614 (23024) hydrogen bonds : bond 0.03546 ( 892) hydrogen bonds : angle 4.67854 ( 2580) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 0.698 Fit side-chains REVERT: A 38 PHE cc_start: 0.6114 (OUTLIER) cc_final: 0.5482 (m-80) REVERT: A 40 PHE cc_start: 0.7599 (t80) cc_final: 0.7015 (t80) REVERT: A 74 TYR cc_start: 0.8534 (m-10) cc_final: 0.8142 (m-80) REVERT: A 105 LYS cc_start: 0.8854 (tttp) cc_final: 0.8569 (ttmt) REVERT: G 74 TYR cc_start: 0.8721 (m-80) cc_final: 0.8246 (m-80) REVERT: G 82 LEU cc_start: 0.9398 (mm) cc_final: 0.9189 (tt) REVERT: G 105 LYS cc_start: 0.8800 (tttm) cc_final: 0.8563 (ttmt) REVERT: C 40 PHE cc_start: 0.7480 (t80) cc_final: 0.7152 (t80) REVERT: C 74 TYR cc_start: 0.8769 (m-80) cc_final: 0.8353 (m-80) outliers start: 24 outliers final: 23 residues processed: 249 average time/residue: 0.1424 time to fit residues: 52.9618 Evaluate side-chains 245 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 215 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 103 optimal weight: 0.0060 chunk 149 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 332 ASN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.110378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.078151 restraints weight = 27231.052| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.31 r_work: 0.2733 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.7293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17020 Z= 0.153 Angle : 0.589 14.071 23024 Z= 0.280 Chirality : 0.046 0.181 2692 Planarity : 0.003 0.035 2988 Dihedral : 4.195 58.239 2386 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.30 % Allowed : 19.62 % Favored : 79.08 % 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: 0.67 (0.18), residues: 2140 helix: 1.48 (0.16), residues: 1012 sheet: 0.76 (0.28), residues: 304 loop : -0.98 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 308 TYR 0.020 0.001 TYR C 51 PHE 0.012 0.001 PHE E 40 TRP 0.009 0.001 TRP E 52 HIS 0.002 0.001 HIS D 286 Details of bonding type rmsd covalent geometry : bond 0.00369 (17020) covalent geometry : angle 0.58883 (23024) hydrogen bonds : bond 0.03836 ( 892) hydrogen bonds : angle 4.72159 ( 2580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5246.65 seconds wall clock time: 90 minutes 8.00 seconds (5408.00 seconds total)