Starting phenix.real_space_refine on Sun May 18 09:20:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8djb_27459/05_2025/8djb_27459.cif Found real_map, /net/cci-nas-00/data/ceres_data/8djb_27459/05_2025/8djb_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_27459/05_2025/8djb_27459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8djb_27459/05_2025/8djb_27459.map" model { file = "/net/cci-nas-00/data/ceres_data/8djb_27459/05_2025/8djb_27459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8djb_27459/05_2025/8djb_27459.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.53, per 1000 atoms: 0.45 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: 3.91 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.00 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: 5.07 Time building geometry restraints manager: 4.52 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: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 34.470 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.250 ------------------------------------------------------------------------------- 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 : 12.93 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP G 52 HIS 0.002 0.001 HIS C 193 PHE 0.006 0.001 PHE C 87 TYR 0.025 0.002 TYR E 51 ARG 0.005 0.000 ARG F 329 Details of bonding type rmsd hydrogen bonds : bond 0.20132 ( 892) hydrogen bonds : angle 7.25013 ( 2580) covalent geometry : bond 0.00540 (17020) covalent geometry : angle 0.72434 (23024) *********************** 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 : 1.854 Fit side-chains REVERT: A 25 LEU cc_start: 0.9053 (mp) cc_final: 0.8780 (tt) 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: 0.8549 (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: 0.7795 (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: 0.8521 (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 25 LEU cc_start: 0.8927 (mp) cc_final: 0.8697 (tt) REVERT: C 80 ILE cc_start: 0.9395 (mt) cc_final: 0.9173 (mt) REVERT: E 25 LEU cc_start: 0.8999 (mp) cc_final: 0.8743 (tt) REVERT: E 38 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.6609 (m-10) outliers start: 128 outliers final: 26 residues processed: 570 average time/residue: 0.3759 time to fit residues: 291.7664 Evaluate side-chains 289 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 256 time to evaluate : 2.015 ------------------------------------------------------------------------------- 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 179 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 89 optimal weight: 0.0470 chunk 54 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 192 optimal weight: 0.0020 overall best weight: 0.4086 ------------------------------------------------------------------------------- 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 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 = 0.3620 r_free = 0.3620 target = 0.117538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.080933 restraints weight = 26782.688| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.28 r_work: 0.2895 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17020 Z= 0.125 Angle : 0.589 12.036 23024 Z= 0.293 Chirality : 0.046 0.153 2692 Planarity : 0.004 0.026 2988 Dihedral : 5.567 59.783 2444 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.66 % Allowed : 13.97 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.18), residues: 2140 helix: 1.01 (0.16), residues: 1040 sheet: 0.50 (0.32), residues: 304 loop : -1.24 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 52 HIS 0.003 0.001 HIS G 39 PHE 0.028 0.001 PHE A 40 TYR 0.036 0.002 TYR C 74 ARG 0.004 0.001 ARG E 22 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 892) hydrogen bonds : angle 5.13937 ( 2580) covalent geometry : bond 0.00269 (17020) covalent geometry : angle 0.58878 (23024) *********************** 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 330 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 281 time to evaluate : 1.789 Fit side-chains REVERT: A 74 TYR cc_start: 0.8415 (m-10) cc_final: 0.7844 (m-80) REVERT: A 82 LEU cc_start: 0.9442 (mm) cc_final: 0.9241 (mm) REVERT: A 104 MET cc_start: 0.8115 (tpp) cc_final: 0.7776 (ttp) REVERT: B 275 LEU cc_start: 0.8540 (mp) cc_final: 0.8230 (mp) REVERT: D 275 LEU cc_start: 0.8603 (tp) cc_final: 0.8329 (mp) REVERT: F 275 LEU cc_start: 0.8492 (mp) cc_final: 0.8157 (mp) REVERT: F 287 ASP cc_start: 0.8447 (m-30) cc_final: 0.8245 (m-30) REVERT: H 170 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8515 (mp) REVERT: G 74 TYR cc_start: 0.8549 (m-80) cc_final: 0.8017 (m-80) REVERT: C 74 TYR cc_start: 0.8565 (m-80) cc_final: 0.8023 (m-80) REVERT: E 74 TYR cc_start: 0.8550 (m-80) cc_final: 0.8036 (m-80) outliers start: 49 outliers final: 29 residues processed: 314 average time/residue: 0.3145 time to fit residues: 143.1998 Evaluate side-chains 260 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 187 SER 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 187 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 187 SER 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 187 SER 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 71 LEU Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 39 HIS 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 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 68 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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** A 219 GLN B 216 ASN D 216 ASN F 216 ASN H 216 ASN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 GLN ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.113579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.076707 restraints weight = 27420.714| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.23 r_work: 0.2806 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17020 Z= 0.203 Angle : 0.644 14.546 23024 Z= 0.325 Chirality : 0.049 0.170 2692 Planarity : 0.004 0.039 2988 Dihedral : 5.162 57.584 2404 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.85 % Allowed : 16.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.18), residues: 2140 helix: 1.03 (0.16), residues: 1016 sheet: 0.25 (0.29), residues: 304 loop : -1.22 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 46 HIS 0.005 0.001 HIS A 39 PHE 0.019 0.001 PHE A 75 TYR 0.028 0.002 TYR G 74 ARG 0.009 0.001 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.04896 ( 892) hydrogen bonds : angle 4.99966 ( 2580) covalent geometry : bond 0.00485 (17020) covalent geometry : angle 0.64393 (23024) *********************** 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 279 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 2.046 Fit side-chains REVERT: A 38 PHE cc_start: 0.6132 (OUTLIER) cc_final: 0.5691 (m-80) REVERT: A 46 TRP cc_start: 0.7341 (t-100) cc_final: 0.7033 (p-90) REVERT: A 74 TYR cc_start: 0.8475 (m-10) cc_final: 0.7992 (m-80) REVERT: A 105 LYS cc_start: 0.8802 (tttt) cc_final: 0.8580 (tttm) REVERT: F 323 LYS cc_start: 0.8741 (mtmt) cc_final: 0.8347 (mtmm) REVERT: H 264 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8882 (ttm) REVERT: G 74 TYR cc_start: 0.8512 (m-80) cc_final: 0.8035 (m-80) REVERT: G 172 LYS cc_start: 0.8867 (mmtm) cc_final: 0.8638 (mmtp) REVERT: C 74 TYR cc_start: 0.8526 (m-80) cc_final: 0.8010 (m-80) REVERT: C 105 LYS cc_start: 0.8858 (tttt) cc_final: 0.8626 (tttm) REVERT: C 172 LYS cc_start: 0.8845 (mmtm) cc_final: 0.8613 (mmtp) REVERT: E 74 TYR cc_start: 0.8465 (m-80) cc_final: 0.8083 (m-80) REVERT: E 105 LYS cc_start: 0.8784 (tttt) cc_final: 0.8548 (tttm) outliers start: 34 outliers final: 13 residues processed: 267 average time/residue: 0.3223 time to fit residues: 124.2790 Evaluate side-chains 231 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 216 time to evaluate : 1.791 ------------------------------------------------------------------------------- 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 87 PHE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 264 MET 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 C residue 38 PHE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 60 VAL 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 162 optimal weight: 3.9990 chunk 206 optimal weight: 0.0370 chunk 49 optimal weight: 0.8980 chunk 134 optimal weight: 0.5980 chunk 121 optimal weight: 0.0270 chunk 136 optimal weight: 0.7980 chunk 35 optimal weight: 0.0870 chunk 9 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3593 r_free = 0.3593 target = 0.115448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.078845 restraints weight = 27338.831| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.26 r_work: 0.2838 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17020 Z= 0.099 Angle : 0.540 13.123 23024 Z= 0.258 Chirality : 0.046 0.175 2692 Planarity : 0.003 0.036 2988 Dihedral : 4.125 58.705 2386 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.47 % Allowed : 17.77 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.18), residues: 2140 helix: 1.45 (0.16), residues: 1016 sheet: 0.34 (0.29), residues: 304 loop : -1.10 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 46 HIS 0.001 0.000 HIS C 39 PHE 0.017 0.001 PHE G 40 TYR 0.020 0.001 TYR A 51 ARG 0.004 0.000 ARG E 135 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 892) hydrogen bonds : angle 4.66794 ( 2580) covalent geometry : bond 0.00211 (17020) covalent geometry : angle 0.53952 (23024) *********************** 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 262 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 1.800 Fit side-chains REVERT: A 38 PHE cc_start: 0.5767 (OUTLIER) cc_final: 0.5441 (m-80) REVERT: A 74 TYR cc_start: 0.8537 (m-10) cc_final: 0.7972 (m-80) REVERT: B 200 LYS cc_start: 0.8909 (ttmm) cc_final: 0.8460 (ttmt) REVERT: D 200 LYS cc_start: 0.8847 (ttmm) cc_final: 0.8476 (ttmt) REVERT: F 200 LYS cc_start: 0.8935 (ttmm) cc_final: 0.8474 (ttmt) REVERT: G 40 PHE cc_start: 0.7501 (t80) cc_final: 0.7257 (t80) REVERT: G 74 TYR cc_start: 0.8624 (m-80) cc_final: 0.8210 (m-80) REVERT: G 90 LEU cc_start: 0.8842 (tt) cc_final: 0.8625 (tp) REVERT: G 105 LYS cc_start: 0.8770 (tttt) cc_final: 0.8526 (tttm) REVERT: G 172 LYS cc_start: 0.8817 (mmtm) cc_final: 0.8591 (mmtp) REVERT: C 40 PHE cc_start: 0.7594 (t80) cc_final: 0.7339 (t80) REVERT: C 74 TYR cc_start: 0.8624 (m-80) cc_final: 0.8175 (m-80) REVERT: C 105 LYS cc_start: 0.8755 (tttt) cc_final: 0.8555 (tttm) REVERT: C 172 LYS cc_start: 0.8812 (mmtm) cc_final: 0.8574 (mmtp) REVERT: E 74 TYR cc_start: 0.8606 (m-80) cc_final: 0.8128 (m-80) REVERT: E 90 LEU cc_start: 0.8879 (tt) cc_final: 0.8656 (tp) outliers start: 27 outliers final: 15 residues processed: 253 average time/residue: 0.2990 time to fit residues: 110.4891 Evaluate side-chains 244 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 228 time to evaluate : 1.765 ------------------------------------------------------------------------------- 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 87 PHE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 95 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 166 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 134 optimal weight: 0.0050 chunk 66 optimal weight: 0.5980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.114835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.079693 restraints weight = 27732.881| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.37 r_work: 0.2833 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.6042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17020 Z= 0.104 Angle : 0.522 13.291 23024 Z= 0.250 Chirality : 0.045 0.144 2692 Planarity : 0.003 0.039 2988 Dihedral : 4.003 59.166 2386 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.12 % Allowed : 17.28 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2140 helix: 1.61 (0.16), residues: 1012 sheet: 0.49 (0.29), residues: 304 loop : -1.03 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 46 HIS 0.007 0.000 HIS A 39 PHE 0.022 0.001 PHE E 40 TYR 0.018 0.001 TYR A 51 ARG 0.004 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 892) hydrogen bonds : angle 4.52082 ( 2580) covalent geometry : bond 0.00233 (17020) covalent geometry : angle 0.52223 (23024) *********************** 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 274 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 1.919 Fit side-chains REVERT: A 38 PHE cc_start: 0.5848 (OUTLIER) cc_final: 0.5319 (m-80) REVERT: A 40 PHE cc_start: 0.8115 (t80) cc_final: 0.7783 (t80) REVERT: A 74 TYR cc_start: 0.8631 (m-10) cc_final: 0.8009 (m-80) REVERT: G 40 PHE cc_start: 0.7421 (t80) cc_final: 0.7112 (t80) REVERT: G 74 TYR cc_start: 0.8703 (m-80) cc_final: 0.8274 (m-80) REVERT: G 105 LYS cc_start: 0.8743 (tttt) cc_final: 0.8495 (tttm) REVERT: G 172 LYS cc_start: 0.8826 (mmtm) cc_final: 0.8591 (mmtp) REVERT: C 40 PHE cc_start: 0.7622 (t80) cc_final: 0.7302 (t80) REVERT: C 74 TYR cc_start: 0.8660 (m-80) cc_final: 0.8283 (m-80) REVERT: C 172 LYS cc_start: 0.8823 (mmtm) cc_final: 0.8584 (mmtp) REVERT: E 74 TYR cc_start: 0.8790 (m-80) cc_final: 0.8305 (m-80) outliers start: 39 outliers final: 22 residues processed: 259 average time/residue: 0.3035 time to fit residues: 115.5059 Evaluate side-chains 245 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 1.901 ------------------------------------------------------------------------------- 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 87 PHE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain F residue 210 GLU 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 95 LEU Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 87 PHE 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 136 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 165 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 192 optimal weight: 0.4980 chunk 178 optimal weight: 0.0050 chunk 58 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3590 r_free = 0.3590 target = 0.115011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.080057 restraints weight = 27386.605| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.37 r_work: 0.2831 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.6255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17020 Z= 0.099 Angle : 0.524 13.380 23024 Z= 0.248 Chirality : 0.045 0.134 2692 Planarity : 0.003 0.038 2988 Dihedral : 3.923 59.384 2386 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.79 % Allowed : 18.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 2140 helix: 1.76 (0.16), residues: 1012 sheet: 0.64 (0.29), residues: 304 loop : -0.96 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 46 HIS 0.001 0.000 HIS F 286 PHE 0.011 0.001 PHE A 40 TYR 0.026 0.001 TYR E 51 ARG 0.004 0.000 ARG H 313 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 892) hydrogen bonds : angle 4.44365 ( 2580) covalent geometry : bond 0.00219 (17020) covalent geometry : angle 0.52449 (23024) *********************** 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 269 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 1.986 Fit side-chains REVERT: A 38 PHE cc_start: 0.5644 (OUTLIER) cc_final: 0.5108 (m-80) REVERT: A 40 PHE cc_start: 0.8117 (t80) cc_final: 0.7716 (t80) REVERT: A 74 TYR cc_start: 0.8643 (m-10) cc_final: 0.8173 (m-10) REVERT: B 281 LEU cc_start: 0.9187 (tt) cc_final: 0.8977 (tp) REVERT: B 300 ASP cc_start: 0.8599 (m-30) cc_final: 0.8340 (t0) REVERT: F 300 ASP cc_start: 0.8586 (m-30) cc_final: 0.8317 (t0) REVERT: G 40 PHE cc_start: 0.7436 (t80) cc_final: 0.7080 (t80) REVERT: G 74 TYR cc_start: 0.8661 (m-80) cc_final: 0.8279 (m-80) REVERT: G 105 LYS cc_start: 0.8788 (tttt) cc_final: 0.8574 (tttp) REVERT: G 172 LYS cc_start: 0.8845 (mmtm) cc_final: 0.8591 (mmtp) REVERT: C 74 TYR cc_start: 0.8739 (m-80) cc_final: 0.8365 (m-80) REVERT: C 172 LYS cc_start: 0.8835 (mmtm) cc_final: 0.8596 (mmtp) REVERT: E 74 TYR cc_start: 0.8779 (m-80) cc_final: 0.8253 (m-80) outliers start: 33 outliers final: 22 residues processed: 257 average time/residue: 0.3208 time to fit residues: 119.7455 Evaluate side-chains 249 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 1.880 ------------------------------------------------------------------------------- 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 87 PHE 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 F residue 210 GLU 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 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 186 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 204 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 4 optimal weight: 0.0270 chunk 61 optimal weight: 0.0670 chunk 69 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 28 optimal weight: 0.0020 chunk 166 optimal weight: 2.9990 chunk 198 optimal weight: 0.5980 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 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 = 0.3597 r_free = 0.3597 target = 0.115564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.079605 restraints weight = 27291.541| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.44 r_work: 0.2843 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.6385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17020 Z= 0.094 Angle : 0.534 14.815 23024 Z= 0.249 Chirality : 0.045 0.133 2692 Planarity : 0.003 0.035 2988 Dihedral : 3.859 59.247 2386 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.63 % Allowed : 18.91 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 2140 helix: 1.85 (0.16), residues: 1012 sheet: 0.72 (0.29), residues: 304 loop : -0.90 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 46 HIS 0.002 0.000 HIS A 39 PHE 0.021 0.001 PHE E 40 TYR 0.020 0.001 TYR E 51 ARG 0.005 0.000 ARG D 308 Details of bonding type rmsd hydrogen bonds : bond 0.03019 ( 892) hydrogen bonds : angle 4.37532 ( 2580) covalent geometry : bond 0.00203 (17020) covalent geometry : angle 0.53381 (23024) *********************** 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 264 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 1.988 Fit side-chains REVERT: A 38 PHE cc_start: 0.5688 (OUTLIER) cc_final: 0.5190 (m-80) REVERT: A 40 PHE cc_start: 0.8111 (t80) cc_final: 0.7612 (t80) REVERT: A 74 TYR cc_start: 0.8601 (m-10) cc_final: 0.8119 (m-80) REVERT: B 300 ASP cc_start: 0.8600 (m-30) cc_final: 0.8367 (t0) REVERT: B 308 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.8173 (ttm-80) REVERT: F 300 ASP cc_start: 0.8570 (m-30) cc_final: 0.8334 (t0) REVERT: G 74 TYR cc_start: 0.8688 (m-80) cc_final: 0.8250 (m-80) REVERT: G 172 LYS cc_start: 0.8794 (mmtm) cc_final: 0.8536 (mmtp) REVERT: C 74 TYR cc_start: 0.8696 (m-80) cc_final: 0.8270 (m-80) REVERT: C 172 LYS cc_start: 0.8768 (mmtm) cc_final: 0.8530 (mmtp) REVERT: E 74 TYR cc_start: 0.8817 (m-80) cc_final: 0.8277 (m-80) REVERT: E 135 ARG cc_start: 0.7713 (mmp80) cc_final: 0.7391 (mpp-170) outliers start: 30 outliers final: 26 residues processed: 254 average time/residue: 0.3148 time to fit residues: 117.6843 Evaluate side-chains 257 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 2.413 ------------------------------------------------------------------------------- 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 50 LEU Chi-restraints excluded: chain A residue 87 PHE 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 F residue 210 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 87 PHE Chi-restraints excluded: chain G residue 95 LEU 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 50 LEU 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 50 LEU Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 186 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 152 optimal weight: 0.0570 chunk 89 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 198 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.114590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.078755 restraints weight = 27316.156| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.38 r_work: 0.2822 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.6520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17020 Z= 0.111 Angle : 0.534 14.011 23024 Z= 0.252 Chirality : 0.045 0.193 2692 Planarity : 0.003 0.035 2988 Dihedral : 3.702 58.856 2384 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.58 % Allowed : 18.91 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 2140 helix: 1.86 (0.16), residues: 1012 sheet: 0.72 (0.29), residues: 304 loop : -0.90 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 46 HIS 0.001 0.000 HIS F 286 PHE 0.009 0.001 PHE B 251 TYR 0.028 0.001 TYR E 51 ARG 0.005 0.000 ARG C 101 Details of bonding type rmsd hydrogen bonds : bond 0.03274 ( 892) hydrogen bonds : angle 4.43150 ( 2580) covalent geometry : bond 0.00257 (17020) covalent geometry : angle 0.53431 (23024) *********************** 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 264 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 2.002 Fit side-chains REVERT: A 40 PHE cc_start: 0.8095 (t80) cc_final: 0.7639 (t80) REVERT: B 308 ARG cc_start: 0.8456 (ttm-80) cc_final: 0.8217 (ttm-80) REVERT: D 308 ARG cc_start: 0.8375 (ttm-80) cc_final: 0.8073 (ttm-80) REVERT: F 308 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.8096 (ttm-80) REVERT: G 74 TYR cc_start: 0.8644 (m-80) cc_final: 0.8268 (m-80) REVERT: G 172 LYS cc_start: 0.8813 (mmtm) cc_final: 0.8563 (mmtp) REVERT: C 74 TYR cc_start: 0.8671 (m-80) cc_final: 0.8255 (m-80) REVERT: C 105 LYS cc_start: 0.8720 (tttp) cc_final: 0.8393 (ttmt) REVERT: C 172 LYS cc_start: 0.8787 (mmtm) cc_final: 0.8544 (mmtp) REVERT: E 74 TYR cc_start: 0.8805 (m-80) cc_final: 0.8290 (m-80) REVERT: E 135 ARG cc_start: 0.7758 (mmp80) cc_final: 0.7454 (mpp-170) outliers start: 29 outliers final: 25 residues processed: 254 average time/residue: 0.3153 time to fit residues: 116.7012 Evaluate side-chains 255 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 1.860 ------------------------------------------------------------------------------- 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 49 SER Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 87 PHE 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 F residue 210 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 95 LEU 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 50 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 318 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 110 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 209 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 60 optimal weight: 0.0970 chunk 131 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.114229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.078146 restraints weight = 27406.384| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.47 r_work: 0.2809 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.6665 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= 0.113 Angle : 0.549 13.515 23024 Z= 0.262 Chirality : 0.045 0.199 2692 Planarity : 0.003 0.036 2988 Dihedral : 3.470 58.564 2382 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.58 % Allowed : 18.97 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.19), residues: 2140 helix: 1.84 (0.16), residues: 1012 sheet: 0.74 (0.29), residues: 304 loop : -0.94 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 52 HIS 0.005 0.000 HIS E 39 PHE 0.022 0.001 PHE E 40 TYR 0.028 0.001 TYR C 51 ARG 0.004 0.000 ARG E 101 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 892) hydrogen bonds : angle 4.44408 ( 2580) covalent geometry : bond 0.00259 (17020) covalent geometry : angle 0.54866 (23024) *********************** 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: 29 poor density : 235 time to evaluate : 2.052 Fit side-chains REVERT: A 21 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8361 (t) REVERT: A 38 PHE cc_start: 0.5697 (OUTLIER) cc_final: 0.5181 (m-80) REVERT: A 40 PHE cc_start: 0.8080 (t80) cc_final: 0.7630 (t80) REVERT: A 105 LYS cc_start: 0.8602 (tttp) cc_final: 0.8247 (ttmt) REVERT: D 308 ARG cc_start: 0.8404 (ttm-80) cc_final: 0.8119 (ttm-80) REVERT: F 308 ARG cc_start: 0.8427 (ttm-80) cc_final: 0.8132 (ttm-80) REVERT: G 73 MET cc_start: 0.8155 (ptm) cc_final: 0.7878 (ptp) REVERT: G 74 TYR cc_start: 0.8709 (m-80) cc_final: 0.8334 (m-80) REVERT: G 105 LYS cc_start: 0.8705 (tttp) cc_final: 0.8378 (ttmt) REVERT: G 172 LYS cc_start: 0.8779 (mmtm) cc_final: 0.8525 (mmtp) REVERT: C 74 TYR cc_start: 0.8739 (m-80) cc_final: 0.8308 (m-80) REVERT: C 105 LYS cc_start: 0.8723 (tttp) cc_final: 0.8387 (ttmt) REVERT: C 172 LYS cc_start: 0.8739 (mmtm) cc_final: 0.8486 (mmtp) REVERT: E 40 PHE cc_start: 0.7336 (t80) cc_final: 0.7047 (t80) REVERT: E 73 MET cc_start: 0.8083 (ptm) cc_final: 0.7846 (ptp) REVERT: E 74 TYR cc_start: 0.8821 (m-80) cc_final: 0.8285 (m-80) REVERT: E 105 LYS cc_start: 0.8729 (tttp) cc_final: 0.8383 (ttmt) REVERT: E 135 ARG cc_start: 0.7734 (mmp80) cc_final: 0.7415 (mpp-170) outliers start: 29 outliers final: 24 residues processed: 254 average time/residue: 0.3184 time to fit residues: 117.8657 Evaluate side-chains 258 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain F residue 210 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 87 PHE Chi-restraints excluded: chain G residue 95 LEU 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 50 LEU 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 50 LEU Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 318 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 36 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 80 optimal weight: 0.4980 chunk 89 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.114004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.077359 restraints weight = 27383.285| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.26 r_work: 0.2817 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17020 Z= 0.115 Angle : 0.557 14.250 23024 Z= 0.264 Chirality : 0.045 0.224 2692 Planarity : 0.003 0.040 2988 Dihedral : 3.463 58.411 2382 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.36 % Allowed : 19.40 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.19), residues: 2140 helix: 1.84 (0.16), residues: 1012 sheet: 0.76 (0.29), residues: 304 loop : -0.95 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 52 HIS 0.002 0.000 HIS E 39 PHE 0.020 0.001 PHE E 40 TYR 0.024 0.001 TYR E 51 ARG 0.004 0.000 ARG C 101 Details of bonding type rmsd hydrogen bonds : bond 0.03301 ( 892) hydrogen bonds : angle 4.45743 ( 2580) covalent geometry : bond 0.00264 (17020) covalent geometry : angle 0.55726 (23024) ********************** 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 254 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 1.873 Fit side-chains REVERT: A 21 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8380 (t) REVERT: A 38 PHE cc_start: 0.5723 (OUTLIER) cc_final: 0.5194 (m-80) REVERT: A 105 LYS cc_start: 0.8571 (tttp) cc_final: 0.8226 (ttmt) REVERT: D 308 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.8074 (ttm-80) REVERT: F 308 ARG cc_start: 0.8429 (ttm-80) cc_final: 0.8124 (ttm-80) REVERT: H 200 LYS cc_start: 0.9118 (ttmm) cc_final: 0.8714 (ttmt) REVERT: G 73 MET cc_start: 0.8105 (ptm) cc_final: 0.7853 (ptp) REVERT: G 74 TYR cc_start: 0.8738 (m-80) cc_final: 0.8348 (m-80) REVERT: G 105 LYS cc_start: 0.8759 (tttp) cc_final: 0.8415 (ttmt) REVERT: G 172 LYS cc_start: 0.8732 (mmtm) cc_final: 0.8477 (mmtp) REVERT: C 74 TYR cc_start: 0.8745 (m-80) cc_final: 0.8306 (m-80) REVERT: C 105 LYS cc_start: 0.8730 (tttp) cc_final: 0.8398 (ttmt) REVERT: C 172 LYS cc_start: 0.8716 (mmtm) cc_final: 0.8421 (mmtp) REVERT: E 40 PHE cc_start: 0.7363 (t80) cc_final: 0.7083 (t80) REVERT: E 74 TYR cc_start: 0.8827 (m-80) cc_final: 0.8307 (m-80) REVERT: E 105 LYS cc_start: 0.8613 (tttp) cc_final: 0.8262 (ttmt) REVERT: E 135 ARG cc_start: 0.7685 (mmp80) cc_final: 0.7388 (mpp-170) outliers start: 25 outliers final: 22 residues processed: 245 average time/residue: 0.3425 time to fit residues: 122.6470 Evaluate side-chains 248 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain F residue 210 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 87 PHE Chi-restraints excluded: chain G residue 95 LEU 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 50 LEU 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 50 LEU Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 186 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 123 optimal weight: 0.0670 chunk 95 optimal weight: 0.5980 chunk 174 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 191 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.114207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.078437 restraints weight = 27454.091| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.41 r_work: 0.2813 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.6852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17020 Z= 0.107 Angle : 0.550 13.839 23024 Z= 0.260 Chirality : 0.045 0.208 2692 Planarity : 0.003 0.039 2988 Dihedral : 3.439 58.121 2382 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.41 % Allowed : 19.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.19), residues: 2140 helix: 1.75 (0.16), residues: 1036 sheet: 0.76 (0.29), residues: 304 loop : -0.92 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 52 HIS 0.002 0.000 HIS B 286 PHE 0.019 0.001 PHE E 40 TYR 0.024 0.001 TYR E 51 ARG 0.004 0.000 ARG C 101 Details of bonding type rmsd hydrogen bonds : bond 0.03174 ( 892) hydrogen bonds : angle 4.42953 ( 2580) covalent geometry : bond 0.00244 (17020) covalent geometry : angle 0.55036 (23024) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9699.24 seconds wall clock time: 167 minutes 51.92 seconds (10071.92 seconds total)