Starting phenix.real_space_refine on Wed Mar 4 11:05:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n4t_24177/03_2026/7n4t_24177.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n4t_24177/03_2026/7n4t_24177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n4t_24177/03_2026/7n4t_24177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n4t_24177/03_2026/7n4t_24177.map" model { file = "/net/cci-nas-00/data/ceres_data/7n4t_24177/03_2026/7n4t_24177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n4t_24177/03_2026/7n4t_24177.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 P 7 5.49 5 S 63 5.16 5 C 8337 2.51 5 N 2121 2.21 5 O 2359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12887 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1808 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "B" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1808 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "C" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1808 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "D" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1808 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "E" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1808 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "F" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1808 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "G" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1808 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Time building chain proxies: 3.36, per 1000 atoms: 0.26 Number of scatterers: 12887 At special positions: 0 Unit cell: (97.37, 98.44, 121.98, 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) S 63 16.00 P 7 15.00 O 2359 8.00 N 2121 7.00 C 8337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 612.3 milliseconds 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 14 sheets defined 48.8% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 111 through 139 removed outlier: 4.902A pdb=" N GLU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N HIS A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 138 " --> pdb=" O TYR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 176 removed outlier: 5.965A pdb=" N ASP A 162 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 250 through 265 Processing helix chain 'A' and resid 300 through 320 Processing helix chain 'B' and resid 112 through 139 removed outlier: 4.919A pdb=" N GLU B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N HIS B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE B 138 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 176 removed outlier: 5.989A pdb=" N ASP B 162 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 removed outlier: 3.604A pdb=" N SER B 223 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 250 through 264 Processing helix chain 'B' and resid 300 through 320 removed outlier: 3.536A pdb=" N HIS B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 139 removed outlier: 3.598A pdb=" N VAL C 129 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N HIS C 137 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE C 138 " --> pdb=" O TYR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 176 removed outlier: 5.461A pdb=" N ASP C 162 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 223 Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 250 through 265 Processing helix chain 'C' and resid 300 through 320 removed outlier: 4.019A pdb=" N HIS C 320 " --> pdb=" O ILE C 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 134 Processing helix chain 'D' and resid 141 through 176 removed outlier: 5.702A pdb=" N ASP D 162 " --> pdb=" O MET D 158 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 229 through 232 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 250 through 265 Processing helix chain 'D' and resid 300 through 320 removed outlier: 3.564A pdb=" N HIS D 320 " --> pdb=" O ILE D 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 134 Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 141 through 176 removed outlier: 5.461A pdb=" N ASP E 162 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 223 Processing helix chain 'E' and resid 229 through 232 Processing helix chain 'E' and resid 247 through 249 No H-bonds generated for 'chain 'E' and resid 247 through 249' Processing helix chain 'E' and resid 250 through 265 Processing helix chain 'E' and resid 300 through 320 removed outlier: 3.641A pdb=" N HIS E 320 " --> pdb=" O ILE E 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 139 removed outlier: 5.272A pdb=" N GLU F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N HIS F 137 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE F 138 " --> pdb=" O TYR F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 160 Processing helix chain 'F' and resid 161 through 176 Processing helix chain 'F' and resid 219 through 223 Processing helix chain 'F' and resid 229 through 232 Processing helix chain 'F' and resid 247 through 264 removed outlier: 4.438A pdb=" N GLY F 252 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL F 253 " --> pdb=" O ALA F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 320 removed outlier: 3.533A pdb=" N HIS F 320 " --> pdb=" O ILE F 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 139 removed outlier: 5.018A pdb=" N GLU G 136 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N HIS G 137 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE G 138 " --> pdb=" O TYR G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 176 removed outlier: 5.506A pdb=" N ASP G 162 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE G 163 " --> pdb=" O ALA G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 223 Processing helix chain 'G' and resid 229 through 232 Processing helix chain 'G' and resid 247 through 249 No H-bonds generated for 'chain 'G' and resid 247 through 249' Processing helix chain 'G' and resid 250 through 265 Processing helix chain 'G' and resid 300 through 320 removed outlier: 3.543A pdb=" N HIS G 320 " --> pdb=" O ILE G 316 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.590A pdb=" N LYS A 205 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ILE A 199 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 7.243A pdb=" N ILE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE B 199 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS B 205 " --> pdb=" O ALA B 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 240 Processing sheet with id=AA4, first strand: chain 'B' and resid 226 through 227 removed outlier: 7.201A pdb=" N ILE C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE C 199 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS C 205 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 235 through 240 removed outlier: 3.837A pdb=" N ARG B 235 " --> pdb=" O THR B 294 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 226 through 227 removed outlier: 7.131A pdb=" N ILE D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ILE D 199 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS D 205 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 235 through 240 removed outlier: 3.745A pdb=" N ARG C 235 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 226 through 227 removed outlier: 7.217A pdb=" N ILE E 203 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE E 199 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS E 205 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 235 through 240 removed outlier: 3.967A pdb=" N ARG D 235 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 226 through 227 removed outlier: 7.283A pdb=" N ILE F 203 " --> pdb=" O ILE F 199 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE F 199 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS F 205 " --> pdb=" O ALA F 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 235 through 240 removed outlier: 3.855A pdb=" N ARG E 235 " --> pdb=" O THR E 294 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 226 through 227 removed outlier: 6.964A pdb=" N ILE G 203 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ILE G 199 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS G 205 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 236 through 240 Processing sheet with id=AB5, first strand: chain 'G' and resid 235 through 240 removed outlier: 3.819A pdb=" N ARG G 235 " --> pdb=" O THR G 294 " (cutoff:3.500A) 707 hydrogen bonds defined for protein. 1998 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: 1.79 Time building geometry restraints manager: 1.53 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: 2031 1.31 - 1.44: 3583 1.44 - 1.56: 7409 1.56 - 1.69: 18 1.69 - 1.81: 119 Bond restraints: 13160 Sorted by residual: bond pdb=" CA GLU D 136 " pdb=" C GLU D 136 " ideal model delta sigma weight residual 1.523 1.592 -0.069 1.35e-02 5.49e+03 2.65e+01 bond pdb=" C GLY D 135 " pdb=" O GLY D 135 " ideal model delta sigma weight residual 1.234 1.186 0.048 1.19e-02 7.06e+03 1.61e+01 bond pdb=" CA TYR B 332 " pdb=" CB TYR B 332 " ideal model delta sigma weight residual 1.529 1.587 -0.058 1.58e-02 4.01e+03 1.36e+01 bond pdb=" C30 PEE F 401 " pdb=" O3 PEE F 401 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C30 PEE A 401 " pdb=" O3 PEE A 401 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 13155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 17604 3.37 - 6.74: 181 6.74 - 10.11: 30 10.11 - 13.48: 7 13.48 - 16.85: 7 Bond angle restraints: 17829 Sorted by residual: angle pdb=" N LEU E 331 " pdb=" CA LEU E 331 " pdb=" C LEU E 331 " ideal model delta sigma weight residual 111.28 123.78 -12.50 1.09e+00 8.42e-01 1.32e+02 angle pdb=" N LEU G 331 " pdb=" CA LEU G 331 " pdb=" C LEU G 331 " ideal model delta sigma weight residual 111.36 123.63 -12.27 1.09e+00 8.42e-01 1.27e+02 angle pdb=" N LEU C 331 " pdb=" CA LEU C 331 " pdb=" C LEU C 331 " ideal model delta sigma weight residual 112.38 121.21 -8.83 1.22e+00 6.72e-01 5.24e+01 angle pdb=" N GLY D 135 " pdb=" CA GLY D 135 " pdb=" C GLY D 135 " ideal model delta sigma weight residual 112.77 103.53 9.24 1.28e+00 6.10e-01 5.21e+01 angle pdb=" N SER G 328 " pdb=" CA SER G 328 " pdb=" C SER G 328 " ideal model delta sigma weight residual 110.42 121.28 -10.86 1.55e+00 4.16e-01 4.91e+01 ... (remaining 17824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.49: 7658 34.49 - 68.99: 119 68.99 - 103.48: 24 103.48 - 137.98: 14 137.98 - 172.47: 18 Dihedral angle restraints: 7833 sinusoidal: 3213 harmonic: 4620 Sorted by residual: dihedral pdb=" CA ASP D 323 " pdb=" C ASP D 323 " pdb=" N PHE D 324 " pdb=" CA PHE D 324 " ideal model delta harmonic sigma weight residual 180.00 152.51 27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" C LEU G 331 " pdb=" N LEU G 331 " pdb=" CA LEU G 331 " pdb=" CB LEU G 331 " ideal model delta harmonic sigma weight residual -122.60 -134.95 12.35 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" CA LEU B 243 " pdb=" C LEU B 243 " pdb=" N ARG B 244 " pdb=" CA ARG B 244 " ideal model delta harmonic sigma weight residual -180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 7830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1945 0.106 - 0.213: 81 0.213 - 0.319: 3 0.319 - 0.425: 7 0.425 - 0.531: 1 Chirality restraints: 2037 Sorted by residual: chirality pdb=" CA LEU G 331 " pdb=" N LEU G 331 " pdb=" C LEU G 331 " pdb=" CB LEU G 331 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.06e+00 chirality pdb=" CA ASN G 335 " pdb=" N ASN G 335 " pdb=" C ASN G 335 " pdb=" CB ASN G 335 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA ASP E 334 " pdb=" N ASP E 334 " pdb=" C ASP E 334 " pdb=" CB ASP E 334 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 2034 not shown) Planarity restraints: 2226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO G 327 " -0.017 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C PRO G 327 " 0.057 2.00e-02 2.50e+03 pdb=" O PRO G 327 " -0.021 2.00e-02 2.50e+03 pdb=" N SER G 328 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 331 " -0.016 2.00e-02 2.50e+03 3.05e-02 9.31e+00 pdb=" C LEU D 331 " 0.053 2.00e-02 2.50e+03 pdb=" O LEU D 331 " -0.019 2.00e-02 2.50e+03 pdb=" N TYR D 332 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 136 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.10e+00 pdb=" C GLU D 136 " 0.052 2.00e-02 2.50e+03 pdb=" O GLU D 136 " -0.020 2.00e-02 2.50e+03 pdb=" N HIS D 137 " -0.017 2.00e-02 2.50e+03 ... (remaining 2223 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1215 2.74 - 3.28: 13217 3.28 - 3.82: 21325 3.82 - 4.36: 25934 4.36 - 4.90: 44847 Nonbonded interactions: 106538 Sorted by model distance: nonbonded pdb=" O LEU A 133 " pdb=" OG SER B 141 " model vdw 2.198 3.040 nonbonded pdb=" OG SER F 284 " pdb=" O PRO F 327 " model vdw 2.205 3.040 nonbonded pdb=" NH2 ARG E 244 " pdb=" OE2 GLU E 246 " model vdw 2.259 3.120 nonbonded pdb=" O LEU C 133 " pdb=" OG SER D 141 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR B 208 " pdb=" OD1 ASP B 210 " model vdw 2.277 3.040 ... (remaining 106533 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.770 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 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 : 0.004 0.073 13160 Z= 0.252 Angle : 0.896 16.852 17829 Z= 0.474 Chirality : 0.052 0.531 2037 Planarity : 0.004 0.061 2226 Dihedral : 18.220 172.474 4865 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.14 % Allowed : 1.01 % Favored : 98.85 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.21), residues: 1589 helix: 2.31 (0.20), residues: 686 sheet: -0.44 (0.35), residues: 210 loop : -1.88 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 271 TYR 0.022 0.002 TYR A 245 PHE 0.018 0.001 PHE A 281 TRP 0.013 0.001 TRP G 184 HIS 0.002 0.000 HIS G 137 Details of bonding type rmsd covalent geometry : bond 0.00447 (13160) covalent geometry : angle 0.89587 (17829) hydrogen bonds : bond 0.12842 ( 707) hydrogen bonds : angle 5.87704 ( 1998) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 290 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 261 MET cc_start: 0.9024 (tmm) cc_final: 0.8816 (tmm) outliers start: 2 outliers final: 0 residues processed: 292 average time/residue: 0.7256 time to fit residues: 226.4212 Evaluate side-chains 243 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 GLN E 137 HIS E 318 GLN F 234 ASN G 318 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.125722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.079544 restraints weight = 17789.986| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.36 r_work: 0.2813 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13160 Z= 0.133 Angle : 0.562 6.260 17829 Z= 0.300 Chirality : 0.044 0.146 2037 Planarity : 0.004 0.065 2226 Dihedral : 21.034 177.913 1939 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.95 % Allowed : 9.16 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.21), residues: 1589 helix: 2.34 (0.19), residues: 686 sheet: -1.06 (0.33), residues: 259 loop : -1.55 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 244 TYR 0.023 0.002 TYR E 174 PHE 0.020 0.001 PHE G 324 TRP 0.017 0.002 TRP D 184 HIS 0.003 0.000 HIS G 137 Details of bonding type rmsd covalent geometry : bond 0.00285 (13160) covalent geometry : angle 0.56214 (17829) hydrogen bonds : bond 0.03883 ( 707) hydrogen bonds : angle 4.55471 ( 1998) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 254 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 263 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8443 (mptm) REVERT: D 247 ASP cc_start: 0.8367 (p0) cc_final: 0.7717 (m-30) REVERT: E 184 TRP cc_start: 0.8139 (p-90) cc_final: 0.7787 (p-90) REVERT: E 250 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8699 (mmtm) REVERT: F 118 MET cc_start: 0.4132 (OUTLIER) cc_final: 0.3469 (tpp) REVERT: F 205 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.9092 (ttmt) REVERT: F 263 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8174 (mptm) REVERT: G 247 ASP cc_start: 0.9018 (p0) cc_final: 0.8615 (p0) REVERT: G 263 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8463 (mptm) outliers start: 27 outliers final: 3 residues processed: 259 average time/residue: 0.7192 time to fit residues: 199.2995 Evaluate side-chains 248 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 239 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain G residue 263 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 32 optimal weight: 0.8980 chunk 88 optimal weight: 0.0980 chunk 24 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.125504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.079251 restraints weight = 17944.288| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.38 r_work: 0.2806 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13160 Z= 0.126 Angle : 0.534 7.133 17829 Z= 0.285 Chirality : 0.043 0.151 2037 Planarity : 0.004 0.064 2226 Dihedral : 19.799 170.341 1939 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.88 % Allowed : 10.61 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.21), residues: 1589 helix: 2.41 (0.19), residues: 686 sheet: -1.13 (0.33), residues: 259 loop : -1.56 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 271 TYR 0.028 0.002 TYR F 245 PHE 0.012 0.001 PHE C 281 TRP 0.018 0.002 TRP G 184 HIS 0.002 0.000 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00273 (13160) covalent geometry : angle 0.53443 (17829) hydrogen bonds : bond 0.03636 ( 707) hydrogen bonds : angle 4.30930 ( 1998) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 250 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 SER cc_start: 0.9120 (m) cc_final: 0.8502 (p) REVERT: B 263 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8460 (mptm) REVERT: B 264 ASN cc_start: 0.9242 (m-40) cc_final: 0.8956 (m-40) REVERT: C 333 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7639 (mmm) REVERT: D 113 THR cc_start: 0.5631 (OUTLIER) cc_final: 0.5396 (m) REVERT: E 184 TRP cc_start: 0.8162 (p-90) cc_final: 0.7865 (p-90) REVERT: E 250 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8734 (mmtm) REVERT: F 118 MET cc_start: 0.4238 (OUTLIER) cc_final: 0.3612 (ptp) REVERT: F 205 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.9126 (ttmt) REVERT: F 334 ASP cc_start: 0.7673 (t0) cc_final: 0.7450 (t0) REVERT: G 247 ASP cc_start: 0.9044 (p0) cc_final: 0.8568 (p0) outliers start: 26 outliers final: 8 residues processed: 259 average time/residue: 0.7688 time to fit residues: 212.7983 Evaluate side-chains 257 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 243 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain G residue 216 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 74 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 10 optimal weight: 0.3980 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 211 ASN E 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.125386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.079394 restraints weight = 17887.653| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.38 r_work: 0.2809 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13160 Z= 0.114 Angle : 0.526 7.153 17829 Z= 0.278 Chirality : 0.043 0.145 2037 Planarity : 0.004 0.062 2226 Dihedral : 19.027 178.580 1939 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.88 % Allowed : 11.26 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.22), residues: 1589 helix: 2.49 (0.20), residues: 693 sheet: -1.12 (0.33), residues: 259 loop : -1.54 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 271 TYR 0.023 0.001 TYR E 174 PHE 0.011 0.001 PHE C 281 TRP 0.019 0.001 TRP G 184 HIS 0.012 0.001 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00243 (13160) covalent geometry : angle 0.52596 (17829) hydrogen bonds : bond 0.03423 ( 707) hydrogen bonds : angle 4.15523 ( 1998) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 SER cc_start: 0.9124 (m) cc_final: 0.8533 (p) REVERT: B 245 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.8735 (m-80) REVERT: B 264 ASN cc_start: 0.9213 (m-40) cc_final: 0.8916 (m-40) REVERT: C 320 HIS cc_start: 0.7997 (OUTLIER) cc_final: 0.6078 (p90) REVERT: C 333 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7568 (mmm) REVERT: D 113 THR cc_start: 0.5694 (OUTLIER) cc_final: 0.5459 (p) REVERT: E 184 TRP cc_start: 0.8139 (p-90) cc_final: 0.7849 (p-90) REVERT: E 205 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.9130 (tttp) REVERT: E 245 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.6719 (t80) REVERT: E 250 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8704 (mmtm) REVERT: E 334 ASP cc_start: 0.7672 (t70) cc_final: 0.7319 (t70) REVERT: F 263 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8212 (mptm) REVERT: F 334 ASP cc_start: 0.7632 (t0) cc_final: 0.7411 (t0) REVERT: G 247 ASP cc_start: 0.9027 (p0) cc_final: 0.8589 (p0) outliers start: 26 outliers final: 8 residues processed: 258 average time/residue: 0.7197 time to fit residues: 198.5809 Evaluate side-chains 253 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 237 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain G residue 216 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 41 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 320 HIS D 211 ASN E 137 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.123681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.076976 restraints weight = 17826.056| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.38 r_work: 0.2764 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13160 Z= 0.156 Angle : 0.558 7.371 17829 Z= 0.298 Chirality : 0.044 0.156 2037 Planarity : 0.004 0.067 2226 Dihedral : 18.659 177.244 1939 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.16 % Allowed : 11.90 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.21), residues: 1589 helix: 2.46 (0.19), residues: 693 sheet: -0.65 (0.36), residues: 217 loop : -1.74 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 271 TYR 0.014 0.002 TYR B 291 PHE 0.012 0.001 PHE D 209 TRP 0.023 0.002 TRP D 184 HIS 0.008 0.001 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00355 (13160) covalent geometry : angle 0.55773 (17829) hydrogen bonds : bond 0.03677 ( 707) hydrogen bonds : angle 4.19196 ( 1998) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 SER cc_start: 0.9195 (m) cc_final: 0.8615 (p) REVERT: B 263 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8437 (mptm) REVERT: B 264 ASN cc_start: 0.9238 (m-40) cc_final: 0.8931 (m-40) REVERT: B 281 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7149 (t80) REVERT: C 320 HIS cc_start: 0.8066 (OUTLIER) cc_final: 0.6642 (p-80) REVERT: E 164 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8698 (mm) REVERT: E 184 TRP cc_start: 0.8185 (p-90) cc_final: 0.7973 (p-90) REVERT: E 205 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.9084 (tttp) REVERT: E 245 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.6632 (t80) REVERT: E 250 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8684 (mmtm) REVERT: E 333 MET cc_start: 0.8576 (mpp) cc_final: 0.8320 (mmt) REVERT: F 118 MET cc_start: 0.3706 (OUTLIER) cc_final: 0.3198 (ptp) REVERT: F 263 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8212 (mptm) REVERT: F 334 ASP cc_start: 0.7592 (t0) cc_final: 0.7366 (t0) REVERT: G 263 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8511 (mptm) REVERT: G 334 ASP cc_start: 0.7651 (t0) cc_final: 0.7449 (t0) outliers start: 30 outliers final: 9 residues processed: 243 average time/residue: 0.7667 time to fit residues: 198.5665 Evaluate side-chains 254 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 263 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 95 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 chunk 114 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 109 optimal weight: 0.0970 chunk 49 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 211 ASN E 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.125174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.079015 restraints weight = 17859.327| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.35 r_work: 0.2800 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13160 Z= 0.113 Angle : 0.532 9.900 17829 Z= 0.281 Chirality : 0.043 0.140 2037 Planarity : 0.004 0.067 2226 Dihedral : 18.308 176.885 1939 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.31 % Allowed : 12.70 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.22), residues: 1589 helix: 2.52 (0.19), residues: 693 sheet: -0.66 (0.36), residues: 217 loop : -1.74 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 271 TYR 0.023 0.001 TYR E 174 PHE 0.012 0.001 PHE F 324 TRP 0.020 0.001 TRP D 184 HIS 0.009 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00240 (13160) covalent geometry : angle 0.53166 (17829) hydrogen bonds : bond 0.03381 ( 707) hydrogen bonds : angle 4.12267 ( 1998) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.6736 (mpt) cc_final: 0.6427 (mpp) REVERT: A 222 SER cc_start: 0.9077 (m) cc_final: 0.8466 (p) REVERT: B 263 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8319 (mptm) REVERT: B 264 ASN cc_start: 0.9090 (m-40) cc_final: 0.8756 (m-40) REVERT: B 281 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7005 (t80) REVERT: C 320 HIS cc_start: 0.7805 (OUTLIER) cc_final: 0.6006 (p90) REVERT: D 177 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8510 (mtp85) REVERT: E 164 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8562 (mm) REVERT: E 184 TRP cc_start: 0.7976 (p-90) cc_final: 0.7730 (p-90) REVERT: E 245 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.6740 (t80) REVERT: E 250 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8556 (mmtm) REVERT: E 256 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8334 (mm-30) REVERT: E 334 ASP cc_start: 0.7657 (t70) cc_final: 0.7376 (t70) REVERT: F 333 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7873 (mmm) REVERT: G 247 ASP cc_start: 0.9086 (p0) cc_final: 0.8669 (p0) REVERT: G 263 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8331 (mptm) REVERT: G 334 ASP cc_start: 0.7569 (t0) cc_final: 0.7240 (t0) outliers start: 32 outliers final: 9 residues processed: 255 average time/residue: 0.7609 time to fit residues: 207.2546 Evaluate side-chains 255 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 237 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 263 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 6 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 35 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: E 137 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.124644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.078396 restraints weight = 17882.671| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.36 r_work: 0.2789 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13160 Z= 0.122 Angle : 0.538 10.683 17829 Z= 0.284 Chirality : 0.043 0.138 2037 Planarity : 0.004 0.065 2226 Dihedral : 17.899 179.742 1939 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.09 % Allowed : 13.28 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.22), residues: 1589 helix: 2.55 (0.19), residues: 693 sheet: -0.62 (0.36), residues: 217 loop : -1.74 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 271 TYR 0.013 0.001 TYR B 174 PHE 0.011 0.001 PHE F 324 TRP 0.022 0.002 TRP D 184 HIS 0.002 0.000 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00266 (13160) covalent geometry : angle 0.53820 (17829) hydrogen bonds : bond 0.03417 ( 707) hydrogen bonds : angle 4.08172 ( 1998) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 SER cc_start: 0.9103 (m) cc_final: 0.8505 (p) REVERT: B 263 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8319 (mptm) REVERT: B 281 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7035 (t80) REVERT: C 320 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.5947 (p90) REVERT: D 140 MET cc_start: 0.6778 (mpm) cc_final: 0.4989 (ptt) REVERT: D 177 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8508 (mtp85) REVERT: D 190 ARG cc_start: 0.8735 (ptm160) cc_final: 0.8517 (ptp-110) REVERT: E 164 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8561 (mm) REVERT: E 184 TRP cc_start: 0.8001 (p-90) cc_final: 0.7768 (p-90) REVERT: E 245 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.6683 (t80) REVERT: E 250 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8558 (mmtm) REVERT: E 256 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8344 (mm-30) REVERT: E 334 ASP cc_start: 0.7584 (t70) cc_final: 0.7245 (t70) REVERT: F 118 MET cc_start: 0.3548 (OUTLIER) cc_final: 0.3077 (ptp) REVERT: F 333 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8031 (mmm) REVERT: G 130 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8223 (mm) REVERT: G 247 ASP cc_start: 0.9106 (p0) cc_final: 0.8743 (p0) REVERT: G 334 ASP cc_start: 0.7624 (t0) cc_final: 0.7260 (t0) outliers start: 29 outliers final: 9 residues processed: 253 average time/residue: 0.7418 time to fit residues: 200.3146 Evaluate side-chains 254 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 115 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 73 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 137 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.121797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.074747 restraints weight = 17812.098| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.38 r_work: 0.2723 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13160 Z= 0.197 Angle : 0.611 9.512 17829 Z= 0.327 Chirality : 0.046 0.178 2037 Planarity : 0.005 0.073 2226 Dihedral : 17.860 179.519 1939 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.73 % Allowed : 14.14 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.21), residues: 1589 helix: 2.47 (0.19), residues: 693 sheet: -0.65 (0.36), residues: 217 loop : -1.75 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 271 TYR 0.016 0.002 TYR A 174 PHE 0.017 0.001 PHE D 209 TRP 0.031 0.003 TRP D 184 HIS 0.005 0.001 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00457 (13160) covalent geometry : angle 0.61050 (17829) hydrogen bonds : bond 0.03943 ( 707) hydrogen bonds : angle 4.18677 ( 1998) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 SER cc_start: 0.9259 (m) cc_final: 0.8684 (p) REVERT: B 140 MET cc_start: 0.7252 (mpt) cc_final: 0.7000 (mpp) REVERT: B 263 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8494 (mptm) REVERT: B 281 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7166 (t80) REVERT: C 320 HIS cc_start: 0.8201 (OUTLIER) cc_final: 0.6270 (p90) REVERT: C 334 ASP cc_start: 0.7534 (t0) cc_final: 0.7129 (t0) REVERT: E 164 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8738 (mm) REVERT: E 245 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.6914 (t80) REVERT: E 250 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8694 (mmtm) REVERT: F 118 MET cc_start: 0.3605 (OUTLIER) cc_final: 0.3093 (ptp) REVERT: F 333 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8192 (mmm) outliers start: 24 outliers final: 6 residues processed: 240 average time/residue: 0.7959 time to fit residues: 203.5835 Evaluate side-chains 235 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 221 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 106 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 211 ASN E 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.121562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.074228 restraints weight = 17869.946| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.35 r_work: 0.2710 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13160 Z= 0.213 Angle : 0.634 10.448 17829 Z= 0.338 Chirality : 0.047 0.183 2037 Planarity : 0.005 0.077 2226 Dihedral : 17.735 179.528 1939 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.44 % Allowed : 14.50 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.21), residues: 1589 helix: 2.44 (0.19), residues: 693 sheet: -0.69 (0.35), residues: 217 loop : -1.80 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 271 TYR 0.019 0.002 TYR C 174 PHE 0.017 0.002 PHE D 209 TRP 0.032 0.003 TRP D 184 HIS 0.004 0.001 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00497 (13160) covalent geometry : angle 0.63363 (17829) hydrogen bonds : bond 0.04021 ( 707) hydrogen bonds : angle 4.20642 ( 1998) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.6477 (mpt) cc_final: 0.5210 (mtp) REVERT: B 140 MET cc_start: 0.7219 (mpt) cc_final: 0.6986 (mpp) REVERT: B 263 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8263 (mptm) REVERT: B 281 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7034 (t80) REVERT: C 245 TYR cc_start: 0.8665 (t80) cc_final: 0.8431 (t80) REVERT: C 246 GLU cc_start: 0.8856 (pp20) cc_final: 0.8599 (pp20) REVERT: C 320 HIS cc_start: 0.8189 (OUTLIER) cc_final: 0.6014 (p90) REVERT: C 334 ASP cc_start: 0.7604 (t0) cc_final: 0.7146 (t0) REVERT: D 140 MET cc_start: 0.6767 (mpm) cc_final: 0.5071 (ptt) REVERT: D 164 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8528 (mm) REVERT: E 245 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.7197 (t80) REVERT: E 250 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8585 (mmtm) REVERT: E 333 MET cc_start: 0.8469 (mpp) cc_final: 0.8139 (mmt) REVERT: F 333 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8149 (mmm) outliers start: 20 outliers final: 8 residues processed: 233 average time/residue: 0.7674 time to fit residues: 190.6787 Evaluate side-chains 232 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 217 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 144 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 94 optimal weight: 0.0970 chunk 111 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 320 HIS D 211 ASN E 137 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.124178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.077878 restraints weight = 17936.542| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.36 r_work: 0.2776 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13160 Z= 0.122 Angle : 0.568 11.946 17829 Z= 0.298 Chirality : 0.043 0.214 2037 Planarity : 0.004 0.073 2226 Dihedral : 17.452 178.715 1939 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.37 % Allowed : 15.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.21), residues: 1589 helix: 2.56 (0.19), residues: 693 sheet: -0.69 (0.35), residues: 217 loop : -1.80 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 271 TYR 0.016 0.001 TYR A 174 PHE 0.013 0.001 PHE F 324 TRP 0.026 0.002 TRP G 184 HIS 0.005 0.001 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00261 (13160) covalent geometry : angle 0.56808 (17829) hydrogen bonds : bond 0.03423 ( 707) hydrogen bonds : angle 4.08405 ( 1998) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.6517 (mpt) cc_final: 0.5186 (ptp) REVERT: A 222 SER cc_start: 0.9089 (m) cc_final: 0.8463 (p) REVERT: A 333 MET cc_start: 0.8629 (mpp) cc_final: 0.8140 (mmm) REVERT: B 222 SER cc_start: 0.8383 (p) cc_final: 0.8175 (p) REVERT: B 263 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8334 (mptm) REVERT: B 281 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7036 (t80) REVERT: C 246 GLU cc_start: 0.8920 (pp20) cc_final: 0.8704 (pp20) REVERT: C 320 HIS cc_start: 0.8202 (OUTLIER) cc_final: 0.6505 (p-80) REVERT: C 334 ASP cc_start: 0.7139 (t0) cc_final: 0.6898 (t0) REVERT: D 140 MET cc_start: 0.6822 (mpm) cc_final: 0.5139 (ptt) REVERT: D 164 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8469 (mm) REVERT: D 247 ASP cc_start: 0.8355 (p0) cc_final: 0.7717 (m-30) REVERT: E 245 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.6872 (t80) REVERT: E 250 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8557 (mmtm) REVERT: E 256 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8378 (mm-30) REVERT: F 118 MET cc_start: 0.3535 (OUTLIER) cc_final: 0.3032 (ptp) REVERT: G 140 MET cc_start: 0.5477 (pmm) cc_final: 0.3645 (ptt) REVERT: G 195 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8753 (p) outliers start: 19 outliers final: 5 residues processed: 243 average time/residue: 0.7628 time to fit residues: 198.1364 Evaluate side-chains 246 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 233 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 61 optimal weight: 0.5980 chunk 46 optimal weight: 7.9990 chunk 10 optimal weight: 0.0370 chunk 151 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 44 optimal weight: 20.0000 overall best weight: 1.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 211 ASN E 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.123217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.076543 restraints weight = 17929.042| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.36 r_work: 0.2752 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13160 Z= 0.151 Angle : 0.586 10.654 17829 Z= 0.310 Chirality : 0.045 0.240 2037 Planarity : 0.004 0.071 2226 Dihedral : 17.345 177.669 1939 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.30 % Allowed : 15.01 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.21), residues: 1589 helix: 2.55 (0.19), residues: 693 sheet: -0.67 (0.36), residues: 217 loop : -1.82 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 271 TYR 0.016 0.002 TYR G 174 PHE 0.013 0.001 PHE B 167 TRP 0.027 0.002 TRP G 184 HIS 0.009 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00341 (13160) covalent geometry : angle 0.58640 (17829) hydrogen bonds : bond 0.03604 ( 707) hydrogen bonds : angle 4.10520 ( 1998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6548.81 seconds wall clock time: 111 minutes 39.49 seconds (6699.49 seconds total)