Starting phenix.real_space_refine on Sun Jun 15 02:14:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8djb_27459/06_2025/8djb_27459.cif Found real_map, /net/cci-nas-00/data/ceres_data/8djb_27459/06_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_27459/06_2025/8djb_27459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8djb_27459/06_2025/8djb_27459.map" model { file = "/net/cci-nas-00/data/ceres_data/8djb_27459/06_2025/8djb_27459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8djb_27459/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.91, per 1000 atoms: 0.47 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: 4.35 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: 2.17 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: 5.04 Time building geometry restraints manager: 5.09 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: 1.100 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: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.200 Process input model: 37.110 Find NCS groups from input model: 0.710 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.610 ------------------------------------------------------------------------------- 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 : 2.088 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: 0.3798 time to fit residues: 296.0553 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 : 2.075 ------------------------------------------------------------------------------- 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: 0.9980 chunk 101 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 192 optimal weight: 0.0020 overall best weight: 0.4686 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.117598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.081814 restraints weight = 26811.862| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.37 r_work: 0.2877 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17020 Z= 0.130 Angle : 0.597 12.707 23024 Z= 0.296 Chirality : 0.046 0.152 2692 Planarity : 0.004 0.025 2988 Dihedral : 5.581 59.696 2444 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.28 % Allowed : 14.24 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.16 (0.18), residues: 2140 helix: 1.00 (0.16), residues: 1040 sheet: 0.51 (0.31), residues: 304 loop : -1.24 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 52 HIS 0.004 0.001 HIS G 39 PHE 0.027 0.001 PHE A 40 TYR 0.036 0.002 TYR C 74 ARG 0.005 0.001 ARG E 22 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 892) hydrogen bonds : angle 5.12714 ( 2580) covalent geometry : bond 0.00284 (17020) covalent geometry : angle 0.59708 (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 322 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 280 time to evaluate : 2.054 Fit side-chains REVERT: A 74 TYR cc_start: 0.8431 (m-10) cc_final: 0.7851 (m-80) REVERT: A 104 MET cc_start: 0.8118 (tpp) cc_final: 0.7779 (ttp) REVERT: A 114 LYS cc_start: 0.7804 (mtpp) cc_final: 0.7601 (mttt) REVERT: B 275 LEU cc_start: 0.8539 (mp) cc_final: 0.8227 (mp) REVERT: B 287 ASP cc_start: 0.8492 (m-30) cc_final: 0.8290 (m-30) REVERT: D 275 LEU cc_start: 0.8606 (tp) cc_final: 0.8325 (mp) REVERT: F 275 LEU cc_start: 0.8474 (mp) cc_final: 0.8141 (mp) REVERT: F 287 ASP cc_start: 0.8472 (m-30) cc_final: 0.8268 (m-30) REVERT: H 170 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8472 (mp) REVERT: G 74 TYR cc_start: 0.8564 (m-80) cc_final: 0.7994 (m-80) REVERT: C 74 TYR cc_start: 0.8582 (m-80) cc_final: 0.8005 (m-80) REVERT: E 74 TYR cc_start: 0.8564 (m-80) cc_final: 0.8029 (m-80) outliers start: 42 outliers final: 24 residues processed: 309 average time/residue: 0.3361 time to fit residues: 149.7476 Evaluate side-chains 256 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 187 SER 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 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 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 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: 0.9990 chunk 151 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 103 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.111924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.074764 restraints weight = 27462.700| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.27 r_work: 0.2775 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.6120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17020 Z= 0.268 Angle : 0.680 12.640 23024 Z= 0.352 Chirality : 0.050 0.306 2692 Planarity : 0.005 0.035 2988 Dihedral : 5.324 57.011 2404 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.90 % Allowed : 16.74 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.18), residues: 2140 helix: 0.91 (0.16), residues: 1012 sheet: 0.29 (0.29), residues: 304 loop : -1.25 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 46 HIS 0.009 0.002 HIS A 39 PHE 0.019 0.002 PHE A 75 TYR 0.027 0.002 TYR G 74 ARG 0.008 0.001 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.05401 ( 892) hydrogen bonds : angle 5.14833 ( 2580) covalent geometry : bond 0.00637 (17020) covalent geometry : angle 0.67980 (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 275 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 2.123 Fit side-chains REVERT: A 38 PHE cc_start: 0.6235 (OUTLIER) cc_final: 0.5714 (m-80) REVERT: A 46 TRP cc_start: 0.7454 (t-100) cc_final: 0.6946 (p-90) REVERT: A 74 TYR cc_start: 0.8485 (m-10) cc_final: 0.7992 (m-80) REVERT: A 114 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8389 (mmtt) REVERT: A 172 LYS cc_start: 0.8867 (mmtm) cc_final: 0.8541 (mmtp) REVERT: B 264 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8944 (ttm) REVERT: D 264 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8958 (ttm) REVERT: F 264 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8935 (ttm) REVERT: H 264 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8949 (ttm) REVERT: G 74 TYR cc_start: 0.8564 (m-80) cc_final: 0.8037 (m-80) REVERT: C 74 TYR cc_start: 0.8567 (m-80) cc_final: 0.8041 (m-80) REVERT: E 74 TYR cc_start: 0.8511 (m-80) cc_final: 0.8075 (m-80) REVERT: E 100 ASN cc_start: 0.8801 (t0) cc_final: 0.8552 (t0) REVERT: E 172 LYS cc_start: 0.8894 (mmtm) cc_final: 0.8651 (mmtm) outliers start: 35 outliers final: 13 residues processed: 264 average time/residue: 0.3354 time to fit residues: 127.1743 Evaluate side-chains 236 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 218 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 87 PHE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain F residue 264 MET 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 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: 0.9980 chunk 206 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 134 optimal weight: 0.4980 chunk 121 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.113721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.080260 restraints weight = 27263.091| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.54 r_work: 0.2795 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17020 Z= 0.119 Angle : 0.553 13.061 23024 Z= 0.265 Chirality : 0.046 0.140 2692 Planarity : 0.003 0.041 2988 Dihedral : 4.233 59.798 2386 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.79 % Allowed : 17.77 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.18), residues: 2140 helix: 1.27 (0.16), residues: 1012 sheet: 0.38 (0.29), residues: 304 loop : -1.18 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 46 HIS 0.011 0.001 HIS A 39 PHE 0.025 0.001 PHE E 40 TYR 0.018 0.001 TYR C 74 ARG 0.009 0.000 ARG G 298 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 892) hydrogen bonds : angle 4.73530 ( 2580) covalent geometry : bond 0.00275 (17020) covalent geometry : angle 0.55273 (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 272 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 2.025 Fit side-chains REVERT: A 38 PHE cc_start: 0.5966 (OUTLIER) cc_final: 0.5495 (m-80) REVERT: A 73 MET cc_start: 0.8095 (ptm) cc_final: 0.7887 (ptp) REVERT: A 74 TYR cc_start: 0.8540 (m-10) cc_final: 0.7973 (m-80) REVERT: A 104 MET cc_start: 0.8330 (tpp) cc_final: 0.7978 (ttp) REVERT: A 105 LYS cc_start: 0.8842 (tttt) cc_final: 0.8600 (tttm) REVERT: A 114 LYS cc_start: 0.8530 (mtpp) cc_final: 0.8315 (mmtt) REVERT: A 172 LYS cc_start: 0.8780 (mmtm) cc_final: 0.8485 (mmtp) REVERT: B 308 ARG cc_start: 0.8639 (ptp-110) cc_final: 0.8399 (ttp80) REVERT: D 200 LYS cc_start: 0.8934 (ttmm) cc_final: 0.8573 (ttmt) REVERT: G 40 PHE cc_start: 0.7551 (t80) cc_final: 0.7298 (t80) REVERT: G 74 TYR cc_start: 0.8628 (m-80) cc_final: 0.8202 (m-80) REVERT: G 105 LYS cc_start: 0.8857 (tttt) cc_final: 0.8632 (tttm) REVERT: C 40 PHE cc_start: 0.7588 (t80) cc_final: 0.7329 (t80) REVERT: C 74 TYR cc_start: 0.8632 (m-80) cc_final: 0.8207 (m-80) REVERT: C 90 LEU cc_start: 0.8837 (tt) cc_final: 0.8624 (tp) REVERT: C 105 LYS cc_start: 0.8862 (tttt) cc_final: 0.8635 (tttm) REVERT: E 105 LYS cc_start: 0.8795 (tttt) cc_final: 0.8545 (tttm) REVERT: E 172 LYS cc_start: 0.8790 (mmtm) cc_final: 0.8474 (mmtp) outliers start: 33 outliers final: 17 residues processed: 261 average time/residue: 0.3150 time to fit residues: 119.6743 Evaluate side-chains 246 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 228 time to evaluate : 1.922 ------------------------------------------------------------------------------- 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 39 HIS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 186 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 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 38 PHE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 186 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 166 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.113088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.076087 restraints weight = 27588.439| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.27 r_work: 0.2797 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.6485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17020 Z= 0.123 Angle : 0.541 13.088 23024 Z= 0.260 Chirality : 0.045 0.140 2692 Planarity : 0.003 0.038 2988 Dihedral : 4.144 59.055 2386 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.30 % Allowed : 18.48 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.50 (0.18), residues: 2140 helix: 1.41 (0.16), residues: 1012 sheet: 0.55 (0.29), residues: 304 loop : -1.12 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 46 HIS 0.004 0.001 HIS A 39 PHE 0.014 0.001 PHE C 40 TYR 0.025 0.002 TYR G 51 ARG 0.005 0.000 ARG G 298 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 892) hydrogen bonds : angle 4.64186 ( 2580) covalent geometry : bond 0.00287 (17020) covalent geometry : angle 0.54097 (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 259 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 235 time to evaluate : 1.937 Fit side-chains REVERT: A 38 PHE cc_start: 0.5605 (OUTLIER) cc_final: 0.5214 (m-80) REVERT: A 74 TYR cc_start: 0.8623 (m-10) cc_final: 0.7976 (m-80) REVERT: A 105 LYS cc_start: 0.8763 (tttt) cc_final: 0.8531 (tttm) REVERT: A 172 LYS cc_start: 0.8702 (mmtm) cc_final: 0.8386 (mmtp) REVERT: B 308 ARG cc_start: 0.8632 (ptp-110) cc_final: 0.8357 (ttp80) REVERT: D 308 ARG cc_start: 0.8565 (ptp-110) cc_final: 0.8234 (ptm160) REVERT: F 308 ARG cc_start: 0.8551 (ptp-110) cc_final: 0.8204 (ptm160) REVERT: H 200 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8629 (ttmt) REVERT: G 40 PHE cc_start: 0.7453 (t80) cc_final: 0.7137 (t80) REVERT: G 74 TYR cc_start: 0.8676 (m-80) cc_final: 0.8234 (m-80) REVERT: G 105 LYS cc_start: 0.8823 (tttt) cc_final: 0.8604 (tttm) REVERT: C 40 PHE cc_start: 0.7598 (t80) cc_final: 0.7281 (t80) REVERT: C 74 TYR cc_start: 0.8689 (m-80) cc_final: 0.8304 (m-80) REVERT: C 105 LYS cc_start: 0.8791 (tttt) cc_final: 0.8565 (tttm) REVERT: E 74 TYR cc_start: 0.8738 (m-80) cc_final: 0.8257 (m-80) REVERT: E 105 LYS cc_start: 0.8755 (tttt) cc_final: 0.8521 (tttm) REVERT: E 172 LYS cc_start: 0.8714 (mmtm) cc_final: 0.8395 (mmtp) outliers start: 24 outliers final: 15 residues processed: 252 average time/residue: 0.3072 time to fit residues: 113.0449 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 : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 215 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 186 GLU Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 95 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 136 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 165 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 178 optimal weight: 0.0020 chunk 58 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3566 r_free = 0.3566 target = 0.113501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.076459 restraints weight = 27333.771| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.31 r_work: 0.2797 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.6633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17020 Z= 0.107 Angle : 0.535 13.858 23024 Z= 0.251 Chirality : 0.045 0.146 2692 Planarity : 0.003 0.038 2988 Dihedral : 4.030 59.207 2386 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.85 % Allowed : 18.48 % Favored : 79.67 % 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: 0.62 (0.18), residues: 2140 helix: 1.43 (0.16), residues: 1032 sheet: 0.64 (0.29), residues: 304 loop : -1.02 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 52 HIS 0.005 0.001 HIS A 39 PHE 0.021 0.001 PHE E 40 TYR 0.017 0.001 TYR E 51 ARG 0.006 0.000 ARG G 298 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 892) hydrogen bonds : angle 4.54921 ( 2580) covalent geometry : bond 0.00244 (17020) covalent geometry : angle 0.53472 (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 274 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 240 time to evaluate : 2.095 Fit side-chains REVERT: A 38 PHE cc_start: 0.5945 (OUTLIER) cc_final: 0.5653 (m-80) REVERT: A 74 TYR cc_start: 0.8620 (m-10) cc_final: 0.8117 (m-80) REVERT: A 105 LYS cc_start: 0.8770 (tttt) cc_final: 0.8540 (tttp) REVERT: A 172 LYS cc_start: 0.8718 (mmtm) cc_final: 0.8413 (mmtp) REVERT: D 200 LYS cc_start: 0.8962 (ttmm) cc_final: 0.8598 (ttmt) REVERT: H 200 LYS cc_start: 0.9042 (ttmm) cc_final: 0.8649 (ttmt) REVERT: G 40 PHE cc_start: 0.7479 (t80) cc_final: 0.7104 (t80) REVERT: G 74 TYR cc_start: 0.8658 (m-80) cc_final: 0.8216 (m-80) REVERT: G 105 LYS cc_start: 0.8829 (tttt) cc_final: 0.8596 (tttp) REVERT: C 40 PHE cc_start: 0.7494 (t80) cc_final: 0.7143 (t80) REVERT: C 74 TYR cc_start: 0.8662 (m-80) cc_final: 0.8263 (m-80) REVERT: C 105 LYS cc_start: 0.8787 (tttt) cc_final: 0.8565 (tttp) REVERT: E 105 LYS cc_start: 0.8766 (tttt) cc_final: 0.8539 (tttp) outliers start: 34 outliers final: 20 residues processed: 266 average time/residue: 0.3191 time to fit residues: 124.9857 Evaluate side-chains 248 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 227 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 54 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 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 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 E residue 38 PHE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 215 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 204 optimal weight: 0.7980 chunk 201 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 61 optimal weight: 0.0970 chunk 69 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 28 optimal weight: 0.0970 chunk 166 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3571 r_free = 0.3571 target = 0.113859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.077089 restraints weight = 27237.322| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.26 r_work: 0.2817 rms_B_bonded: 2.70 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: 0.8690 moved from start: 0.6739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17020 Z= 0.100 Angle : 0.539 13.758 23024 Z= 0.252 Chirality : 0.045 0.187 2692 Planarity : 0.003 0.052 2988 Dihedral : 3.956 58.721 2386 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.47 % Allowed : 18.21 % Favored : 80.33 % 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: 0.76 (0.19), residues: 2140 helix: 1.58 (0.16), residues: 1032 sheet: 0.71 (0.29), residues: 304 loop : -0.98 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 46 HIS 0.003 0.000 HIS A 39 PHE 0.011 0.001 PHE G 54 TYR 0.025 0.001 TYR E 51 ARG 0.017 0.000 ARG D 308 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 892) hydrogen bonds : angle 4.48524 ( 2580) covalent geometry : bond 0.00224 (17020) covalent geometry : angle 0.53909 (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 262 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 2.124 Fit side-chains REVERT: A 38 PHE cc_start: 0.5866 (OUTLIER) cc_final: 0.5512 (m-80) REVERT: A 54 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8844 (m-80) REVERT: A 74 TYR cc_start: 0.8591 (m-10) cc_final: 0.8092 (m-80) REVERT: A 172 LYS cc_start: 0.8627 (mmtm) cc_final: 0.8414 (mmtm) REVERT: D 200 LYS cc_start: 0.8940 (ttmm) cc_final: 0.8565 (ttmt) REVERT: D 308 ARG cc_start: 0.8531 (ttm110) cc_final: 0.8256 (ttm-80) REVERT: F 308 ARG cc_start: 0.8565 (ttm110) cc_final: 0.8290 (ttm-80) REVERT: H 200 LYS cc_start: 0.9022 (ttmm) cc_final: 0.8608 (ttmt) REVERT: G 74 TYR cc_start: 0.8730 (m-80) cc_final: 0.8292 (m-80) REVERT: C 40 PHE cc_start: 0.7462 (t80) cc_final: 0.7077 (t80) REVERT: C 74 TYR cc_start: 0.8660 (m-80) cc_final: 0.8268 (m-80) outliers start: 27 outliers final: 16 residues processed: 256 average time/residue: 0.3216 time to fit residues: 120.3479 Evaluate side-chains 244 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 226 time to evaluate : 2.183 ------------------------------------------------------------------------------- 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 54 PHE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain D residue 301 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 186 GLU Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 215 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 25 optimal weight: 0.0020 chunk 64 optimal weight: 0.3980 chunk 133 optimal weight: 0.4980 chunk 171 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 198 optimal weight: 1.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.114027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.077167 restraints weight = 27162.824| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.30 r_work: 0.2819 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.6816 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= 0.101 Angle : 0.552 14.261 23024 Z= 0.260 Chirality : 0.045 0.183 2692 Planarity : 0.003 0.045 2988 Dihedral : 3.925 58.957 2386 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.09 % Allowed : 18.91 % Favored : 80.00 % 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: 0.83 (0.19), residues: 2140 helix: 1.64 (0.16), residues: 1032 sheet: 0.75 (0.29), residues: 304 loop : -0.97 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 46 HIS 0.003 0.000 HIS A 39 PHE 0.009 0.001 PHE C 40 TYR 0.024 0.001 TYR C 51 ARG 0.010 0.000 ARG D 308 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 892) hydrogen bonds : angle 4.44567 ( 2580) covalent geometry : bond 0.00224 (17020) covalent geometry : angle 0.55208 (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 254 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 1.953 Fit side-chains REVERT: A 38 PHE cc_start: 0.5878 (OUTLIER) cc_final: 0.5538 (m-80) REVERT: D 200 LYS cc_start: 0.8946 (ttmm) cc_final: 0.8592 (ttmt) REVERT: H 200 LYS cc_start: 0.9041 (ttmm) cc_final: 0.8622 (ttmt) REVERT: G 74 TYR cc_start: 0.8765 (m-80) cc_final: 0.8278 (m-80) REVERT: C 40 PHE cc_start: 0.7455 (t80) cc_final: 0.7053 (t80) REVERT: C 74 TYR cc_start: 0.8672 (m-80) cc_final: 0.8271 (m-80) REVERT: C 313 ARG cc_start: 0.8190 (tpp80) cc_final: 0.7946 (mmm-85) REVERT: E 135 ARG cc_start: 0.7736 (mmp80) cc_final: 0.7445 (mpp-170) outliers start: 20 outliers final: 17 residues processed: 249 average time/residue: 0.3204 time to fit residues: 116.0405 Evaluate side-chains 246 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 228 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 215 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 186 GLU Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 215 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 110 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 201 optimal weight: 0.7980 chunk 103 optimal weight: 0.0030 chunk 209 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.113747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.076797 restraints weight = 27360.449| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.31 r_work: 0.2811 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.6909 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= 0.106 Angle : 0.554 13.629 23024 Z= 0.260 Chirality : 0.045 0.188 2692 Planarity : 0.003 0.037 2988 Dihedral : 3.754 59.354 2384 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.92 % Allowed : 19.46 % Favored : 79.62 % 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: 0.86 (0.19), residues: 2140 helix: 1.63 (0.16), residues: 1032 sheet: 0.82 (0.29), residues: 304 loop : -0.94 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 46 HIS 0.003 0.000 HIS A 39 PHE 0.009 0.001 PHE D 251 TYR 0.022 0.001 TYR G 51 ARG 0.003 0.000 ARG G 298 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 892) hydrogen bonds : angle 4.46193 ( 2580) covalent geometry : bond 0.00239 (17020) covalent geometry : angle 0.55431 (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 253 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 236 time to evaluate : 2.172 Fit side-chains REVERT: A 38 PHE cc_start: 0.5868 (OUTLIER) cc_final: 0.5511 (m-80) REVERT: A 74 TYR cc_start: 0.8446 (m-10) cc_final: 0.8052 (m-10) REVERT: B 308 ARG cc_start: 0.8516 (ttp80) cc_final: 0.8179 (ttp80) REVERT: H 200 LYS cc_start: 0.9062 (ttmm) cc_final: 0.8643 (ttmt) REVERT: G 74 TYR cc_start: 0.8814 (m-80) cc_final: 0.8296 (m-80) REVERT: G 105 LYS cc_start: 0.8747 (tttp) cc_final: 0.8407 (ttmt) REVERT: C 40 PHE cc_start: 0.7433 (t80) cc_final: 0.7034 (t80) REVERT: C 74 TYR cc_start: 0.8758 (m-80) cc_final: 0.8345 (m-80) REVERT: C 105 LYS cc_start: 0.8748 (tttp) cc_final: 0.8421 (ttmt) REVERT: C 313 ARG cc_start: 0.8297 (tpp80) cc_final: 0.8072 (mmm-85) REVERT: E 73 MET cc_start: 0.8154 (ptm) cc_final: 0.7947 (ptp) REVERT: E 105 LYS cc_start: 0.8746 (tttp) cc_final: 0.8413 (ttmt) REVERT: E 135 ARG cc_start: 0.7697 (mmp80) cc_final: 0.7411 (mpp-170) outliers start: 17 outliers final: 16 residues processed: 248 average time/residue: 0.3337 time to fit residues: 119.6366 Evaluate side-chains 246 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 229 time to evaluate : 1.926 ------------------------------------------------------------------------------- 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 186 GLU Chi-restraints excluded: chain A residue 215 GLU 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 87 PHE Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 215 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 36 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 67 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3568 r_free = 0.3568 target = 0.113698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.077123 restraints weight = 27320.677| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.24 r_work: 0.2821 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.6973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17020 Z= 0.108 Angle : 0.566 14.147 23024 Z= 0.265 Chirality : 0.045 0.196 2692 Planarity : 0.003 0.041 2988 Dihedral : 3.752 59.107 2384 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.30 % Allowed : 19.46 % 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: 0.87 (0.19), residues: 2140 helix: 1.66 (0.16), residues: 1032 sheet: 0.86 (0.28), residues: 304 loop : -0.97 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 46 HIS 0.003 0.000 HIS A 39 PHE 0.008 0.001 PHE C 40 TYR 0.025 0.001 TYR E 74 ARG 0.005 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 892) hydrogen bonds : angle 4.46311 ( 2580) covalent geometry : bond 0.00245 (17020) covalent geometry : angle 0.56618 (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 253 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 2.179 Fit side-chains revert: symmetry clash REVERT: A 38 PHE cc_start: 0.5869 (OUTLIER) cc_final: 0.5514 (m-80) REVERT: A 105 LYS cc_start: 0.8644 (tttp) cc_final: 0.8292 (ttmt) REVERT: H 200 LYS cc_start: 0.9056 (ttmm) cc_final: 0.8620 (ttmt) REVERT: G 74 TYR cc_start: 0.8850 (m-80) cc_final: 0.8276 (m-80) REVERT: G 105 LYS cc_start: 0.8752 (tttp) cc_final: 0.8416 (ttmt) REVERT: G 172 LYS cc_start: 0.8742 (mmtp) cc_final: 0.8491 (mmtp) REVERT: C 40 PHE cc_start: 0.7475 (t80) cc_final: 0.7078 (t80) REVERT: C 74 TYR cc_start: 0.8787 (m-80) cc_final: 0.8327 (m-80) REVERT: C 105 LYS cc_start: 0.8724 (tttp) cc_final: 0.8403 (ttmt) REVERT: C 172 LYS cc_start: 0.8731 (mmtp) cc_final: 0.8478 (mmtp) REVERT: C 313 ARG cc_start: 0.8275 (tpp80) cc_final: 0.8047 (mmm-85) REVERT: E 73 MET cc_start: 0.8146 (ptm) cc_final: 0.7935 (ptp) REVERT: E 74 TYR cc_start: 0.8738 (m-80) cc_final: 0.8402 (m-80) REVERT: E 105 LYS cc_start: 0.8715 (tttp) cc_final: 0.8391 (ttmt) REVERT: E 135 ARG cc_start: 0.7612 (mmp80) cc_final: 0.7346 (mpp-170) outliers start: 24 outliers final: 20 residues processed: 246 average time/residue: 0.3448 time to fit residues: 123.5163 Evaluate side-chains 247 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 226 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 215 GLU 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 G residue 334 ILE Chi-restraints excluded: chain C residue 38 PHE 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 C residue 334 ILE Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 334 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 123 optimal weight: 0.0970 chunk 95 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN ** 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 = 0.3547 r_free = 0.3547 target = 0.112233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.076223 restraints weight = 27446.265| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.46 r_work: 0.2770 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.7091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17020 Z= 0.146 Angle : 0.573 13.765 23024 Z= 0.272 Chirality : 0.046 0.189 2692 Planarity : 0.004 0.041 2988 Dihedral : 3.851 58.864 2384 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.30 % Allowed : 19.40 % Favored : 79.29 % 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: 0.75 (0.19), residues: 2140 helix: 1.53 (0.16), residues: 1032 sheet: 0.85 (0.28), residues: 304 loop : -1.01 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 46 HIS 0.003 0.001 HIS A 39 PHE 0.008 0.001 PHE C 40 TYR 0.022 0.001 TYR E 74 ARG 0.013 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 892) hydrogen bonds : angle 4.54973 ( 2580) covalent geometry : bond 0.00353 (17020) covalent geometry : angle 0.57343 (23024) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10350.32 seconds wall clock time: 178 minutes 23.82 seconds (10703.82 seconds total)