Starting phenix.real_space_refine on Fri Jul 3 08:27:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n4t_24177/07_2026/7n4t_24177.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n4t_24177/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7n4t_24177/07_2026/7n4t_24177.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n4t_24177/07_2026/7n4t_24177.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n4t_24177/07_2026/7n4t_24177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n4t_24177/07_2026/7n4t_24177.map" model { file = "/net/cci-nas-00/data/ceres_data/7n4t_24177/07_2026/7n4t_24177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n4t_24177/07_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-6108/lib/python3.11/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: 2.43, per 1000 atoms: 0.19 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: 0.97 Conformation dependent library (CDL) restraints added in 640.8 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: 0.33 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: 2.00 Time building geometry restraints manager: 1.30 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: 7641 34.49 - 68.99: 91 68.99 - 103.48: 20 103.48 - 137.98: 6 137.98 - 172.47: 5 Dihedral angle restraints: 7763 sinusoidal: 3143 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 7760 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: 1.070 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.100 Find NCS groups from input model: 0.260 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:8.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 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 : 14.859 172.474 4795 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/Z covalent geometry : bond 0.00447 / 0.25 (13160) covalent geometry : angle 0.89587 / 0.47 (17829) hydrogen bonds : bond 0.12842 / 8.52 ( 707) hydrogen bonds : angle 5.87704 / 4.24 ( 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 : 0.419 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: 0.6179 time to fit residues: 193.3161 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 : 0.329 ------------------------------------------------------------------------------- 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... 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 = 0.3666 r_free = 0.3666 target = 0.125823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.079760 restraints weight = 17775.515| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.36 r_work: 0.2813 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13160 Z= 0.132 Angle : 0.562 6.411 17829 Z= 0.301 Chirality : 0.044 0.169 2037 Planarity : 0.004 0.065 2226 Dihedral : 13.038 179.236 1869 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.02 % Allowed : 8.95 % Favored : 89.03 % 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: 2.32 (0.19), residues: 686 sheet: -1.04 (0.33), residues: 259 loop : -1.54 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 244 TYR 0.025 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/Z covalent geometry : bond 0.00280 / 0.13 (13160) covalent geometry : angle 0.56227 / 0.30 (17829) hydrogen bonds : bond 0.03780 / 2.56 ( 707) hydrogen bonds : angle 4.47988 / 3.17 ( 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 283 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 263 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8484 (mptm) REVERT: D 247 ASP cc_start: 0.8402 (p0) cc_final: 0.7795 (m-30) REVERT: E 184 TRP cc_start: 0.8173 (p-90) cc_final: 0.7826 (p-90) REVERT: E 250 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8717 (mmtm) REVERT: F 118 MET cc_start: 0.3950 (OUTLIER) cc_final: 0.3391 (ptt) REVERT: F 205 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9126 (ttmt) REVERT: F 263 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8189 (mptm) REVERT: G 247 ASP cc_start: 0.9029 (p0) cc_final: 0.8609 (p0) REVERT: G 263 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8504 (mptm) outliers start: 28 outliers final: 3 residues processed: 261 average time/residue: 0.6047 time to fit residues: 169.4349 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 : 0.450 ------------------------------------------------------------------------------- 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: 4.9990 chunk 88 optimal weight: 9.9990 chunk 24 optimal weight: 30.0000 chunk 23 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 137 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.119745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.072121 restraints weight = 18005.863| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.34 r_work: 0.2669 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 13160 Z= 0.314 Angle : 0.693 8.265 17829 Z= 0.379 Chirality : 0.051 0.218 2037 Planarity : 0.006 0.085 2226 Dihedral : 12.434 174.510 1869 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.31 % Allowed : 10.82 % Favored : 86.87 % 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: 0.21 (0.21), residues: 1589 helix: 2.21 (0.19), residues: 686 sheet: -0.78 (0.35), residues: 217 loop : -1.80 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 271 TYR 0.025 0.002 TYR F 245 PHE 0.025 0.002 PHE D 209 TRP 0.036 0.004 TRP D 184 HIS 0.013 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00744 / 0.31 (13160) covalent geometry : angle 0.69328 / 0.38 (17829) hydrogen bonds : bond 0.04902 / 3.33 ( 707) hydrogen bonds : angle 4.59606 / 3.25 ( 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 265 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: B 140 MET cc_start: 0.7229 (mpt) cc_final: 0.6338 (mpp) REVERT: B 263 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8484 (mptm) REVERT: B 281 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7203 (t80) REVERT: C 320 HIS cc_start: 0.8116 (OUTLIER) cc_final: 0.6911 (p-80) REVERT: C 333 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7722 (mmm) REVERT: D 113 THR cc_start: 0.5675 (OUTLIER) cc_final: 0.5464 (m) REVERT: D 227 GLU cc_start: 0.8851 (tt0) cc_final: 0.7465 (tt0) REVERT: E 212 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.6826 (mtm180) REVERT: E 245 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.6761 (t80) REVERT: E 250 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8760 (mmtm) REVERT: E 334 ASP cc_start: 0.7807 (t0) cc_final: 0.7588 (t0) REVERT: F 118 MET cc_start: 0.4243 (OUTLIER) cc_final: 0.3566 (ptp) REVERT: F 263 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8325 (mptm) REVERT: G 247 ASP cc_start: 0.9270 (p0) cc_final: 0.8807 (p0) REVERT: G 263 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8568 (mptm) REVERT: G 334 ASP cc_start: 0.7616 (t0) cc_final: 0.7379 (t0) outliers start: 32 outliers final: 6 residues processed: 243 average time/residue: 0.6294 time to fit residues: 164.0175 Evaluate side-chains 240 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 223 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET 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 C residue 333 MET Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 232 MET 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 0.0670 chunk 111 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 30.0000 chunk 4 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.124143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.077213 restraints weight = 17747.587| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.26 r_work: 0.2754 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13160 Z= 0.130 Angle : 0.545 6.743 17829 Z= 0.294 Chirality : 0.044 0.165 2037 Planarity : 0.004 0.069 2226 Dihedral : 11.536 174.078 1869 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.95 % Allowed : 11.76 % Favored : 86.29 % 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: 0.35 (0.21), residues: 1589 helix: 2.39 (0.20), residues: 686 sheet: -0.75 (0.35), residues: 217 loop : -1.79 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 271 TYR 0.022 0.001 TYR E 174 PHE 0.011 0.001 PHE C 281 TRP 0.022 0.002 TRP G 184 HIS 0.002 0.000 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (13160) covalent geometry : angle 0.54471 / 0.29 (17829) hydrogen bonds : bond 0.03684 / 2.50 ( 707) hydrogen bonds : angle 4.29323 / 3.03 ( 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 275 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 248 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 263 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8215 (mptm) REVERT: B 264 ASN cc_start: 0.9115 (m-40) cc_final: 0.8768 (m-40) REVERT: C 184 TRP cc_start: 0.8088 (p-90) cc_final: 0.7851 (p-90) REVERT: C 320 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.6629 (p-80) REVERT: C 333 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7061 (mpp) REVERT: D 113 THR cc_start: 0.5687 (OUTLIER) cc_final: 0.5479 (m) REVERT: D 247 ASP cc_start: 0.8404 (p0) cc_final: 0.7671 (m-30) REVERT: E 250 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8515 (mmtm) REVERT: E 334 ASP cc_start: 0.7879 (t0) cc_final: 0.7529 (t0) REVERT: G 247 ASP cc_start: 0.9100 (p0) cc_final: 0.8646 (p0) REVERT: G 334 ASP cc_start: 0.7413 (t0) cc_final: 0.7130 (t0) outliers start: 27 outliers final: 7 residues processed: 261 average time/residue: 0.6414 time to fit residues: 179.2129 Evaluate side-chains 244 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 232 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 263 LYS 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 212 ARG Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 118 MET 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: 0.9980 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.122434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.075316 restraints weight = 17850.190| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.26 r_work: 0.2716 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13160 Z= 0.176 Angle : 0.588 7.269 17829 Z= 0.315 Chirality : 0.045 0.167 2037 Planarity : 0.005 0.074 2226 Dihedral : 11.131 173.295 1869 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.73 % Allowed : 12.84 % Favored : 85.43 % 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: 0.36 (0.21), residues: 1589 helix: 2.38 (0.19), residues: 693 sheet: -0.73 (0.35), residues: 217 loop : -1.81 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 271 TYR 0.016 0.002 TYR A 174 PHE 0.015 0.001 PHE D 209 TRP 0.027 0.002 TRP D 184 HIS 0.003 0.000 HIS C 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (13160) covalent geometry : angle 0.58754 / 0.31 (17829) hydrogen bonds : bond 0.03976 / 2.70 ( 707) hydrogen bonds : angle 4.30841 / 3.04 ( 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 258 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 234 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.6754 (mpt) cc_final: 0.6476 (mpp) REVERT: B 264 ASN cc_start: 0.9141 (m-40) cc_final: 0.8789 (m-40) REVERT: B 281 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7039 (t80) REVERT: C 184 TRP cc_start: 0.8161 (p-90) cc_final: 0.7909 (p-90) REVERT: C 246 GLU cc_start: 0.8908 (pp20) cc_final: 0.8698 (pp20) REVERT: C 320 HIS cc_start: 0.7819 (OUTLIER) cc_final: 0.6596 (p-80) REVERT: C 333 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7559 (mmm) REVERT: E 164 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8610 (mm) REVERT: E 245 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.6822 (t80) REVERT: E 250 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8527 (mmtm) REVERT: F 333 MET cc_start: 0.8143 (tpp) cc_final: 0.7940 (mmm) REVERT: G 247 ASP cc_start: 0.9228 (p0) cc_final: 0.8809 (p0) REVERT: G 334 ASP cc_start: 0.7447 (t0) cc_final: 0.7071 (t0) outliers start: 24 outliers final: 9 residues processed: 245 average time/residue: 0.6523 time to fit residues: 170.6197 Evaluate side-chains 245 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 230 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 VAL 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 C residue 333 MET Chi-restraints excluded: chain D residue 158 MET 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 G residue 158 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 95 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 50 optimal weight: 0.4980 chunk 114 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.123497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.076678 restraints weight = 17737.146| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.26 r_work: 0.2745 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13160 Z= 0.144 Angle : 0.568 10.556 17829 Z= 0.302 Chirality : 0.044 0.159 2037 Planarity : 0.004 0.070 2226 Dihedral : 10.645 173.680 1869 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.02 % Allowed : 13.49 % Favored : 84.49 % 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: 0.40 (0.21), residues: 1589 helix: 2.43 (0.19), residues: 693 sheet: -0.72 (0.35), residues: 217 loop : -1.81 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 271 TYR 0.024 0.001 TYR E 174 PHE 0.012 0.001 PHE F 324 TRP 0.025 0.002 TRP G 184 HIS 0.002 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (13160) covalent geometry : angle 0.56824 / 0.30 (17829) hydrogen bonds : bond 0.03679 / 2.49 ( 707) hydrogen bonds : angle 4.20143 / 2.97 ( 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 263 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 235 time to evaluate : 0.502 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: 0.6613 (mpt) cc_final: 0.6343 (mpp) REVERT: B 263 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8193 (mptm) REVERT: B 264 ASN cc_start: 0.9117 (m-40) cc_final: 0.8772 (m-40) REVERT: B 281 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7011 (t80) REVERT: C 184 TRP cc_start: 0.8107 (p-90) cc_final: 0.7872 (p-90) REVERT: C 320 HIS cc_start: 0.7807 (OUTLIER) cc_final: 0.6493 (p-80) REVERT: D 177 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8459 (mtp85) REVERT: E 164 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8561 (mm) REVERT: E 245 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.6710 (t80) REVERT: E 250 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8522 (mmtm) REVERT: F 140 MET cc_start: 0.6387 (pmm) cc_final: 0.6159 (pmm) REVERT: G 247 ASP cc_start: 0.9160 (p0) cc_final: 0.8704 (p0) REVERT: G 334 ASP cc_start: 0.7517 (t0) cc_final: 0.7076 (t0) outliers start: 28 outliers final: 8 residues processed: 248 average time/residue: 0.6684 time to fit residues: 177.0628 Evaluate side-chains 244 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 229 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 C residue 333 MET 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 E residue 281 PHE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 216 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 6 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 103 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.124816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.078202 restraints weight = 17730.141| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.27 r_work: 0.2778 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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 0.029 13160 Z= 0.118 Angle : 0.542 10.164 17829 Z= 0.286 Chirality : 0.043 0.149 2037 Planarity : 0.004 0.067 2226 Dihedral : 10.164 173.510 1869 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.09 % Allowed : 14.07 % Favored : 83.84 % 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: 0.45 (0.21), residues: 1589 helix: 2.50 (0.19), residues: 693 sheet: -0.70 (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 0.001 TYR A 174 PHE 0.014 0.001 PHE F 324 TRP 0.022 0.002 TRP D 184 HIS 0.002 0.000 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (13160) covalent geometry : angle 0.54163 / 0.29 (17829) hydrogen bonds : bond 0.03458 / 2.35 ( 707) hydrogen bonds : angle 4.12467 / 2.91 ( 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 264 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 SER cc_start: 0.8403 (p) cc_final: 0.8192 (p) REVERT: B 263 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8245 (mptm) REVERT: B 281 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.6980 (t80) REVERT: C 184 TRP cc_start: 0.8076 (p-90) cc_final: 0.7847 (p-90) REVERT: C 245 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7081 (t80) REVERT: C 246 GLU cc_start: 0.8905 (pp20) cc_final: 0.8656 (pp20) REVERT: C 320 HIS cc_start: 0.7814 (OUTLIER) cc_final: 0.7517 (p90) REVERT: D 177 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8460 (mtp85) REVERT: E 164 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8541 (mm) REVERT: E 184 TRP cc_start: 0.8121 (p-90) cc_final: 0.7822 (p-90) REVERT: E 245 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.6348 (t80) REVERT: E 250 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8498 (mmtm) REVERT: E 256 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8282 (mm-30) REVERT: E 281 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.7475 (t80) REVERT: F 140 MET cc_start: 0.6254 (pmm) cc_final: 0.6037 (pmm) REVERT: G 247 ASP cc_start: 0.9079 (p0) cc_final: 0.8686 (p0) REVERT: G 334 ASP cc_start: 0.7646 (t0) cc_final: 0.7174 (t0) outliers start: 29 outliers final: 7 residues processed: 249 average time/residue: 0.6496 time to fit residues: 173.1940 Evaluate side-chains 243 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 227 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 245 TYR 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 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 E residue 281 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 115 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 131 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.124498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.077985 restraints weight = 17643.300| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.26 r_work: 0.2767 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2306 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= 0.126 Angle : 0.556 8.871 17829 Z= 0.294 Chirality : 0.043 0.145 2037 Planarity : 0.004 0.064 2226 Dihedral : 9.904 172.606 1869 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.73 % Allowed : 14.57 % Favored : 83.69 % 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: 0.47 (0.22), residues: 1589 helix: 2.53 (0.19), residues: 693 sheet: -0.69 (0.36), residues: 217 loop : -1.81 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 271 TYR 0.022 0.001 TYR E 174 PHE 0.013 0.001 PHE F 324 TRP 0.022 0.002 TRP D 184 HIS 0.002 0.000 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (13160) covalent geometry : angle 0.55631 / 0.29 (17829) hydrogen bonds : bond 0.03473 / 2.36 ( 707) hydrogen bonds : angle 4.10230 / 2.90 ( 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 255 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 SER cc_start: 0.8409 (p) cc_final: 0.8199 (p) REVERT: B 263 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8251 (mptm) REVERT: B 281 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.6972 (t80) REVERT: C 184 TRP cc_start: 0.7974 (p-90) cc_final: 0.7733 (p-90) REVERT: C 245 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.7177 (t80) REVERT: C 246 GLU cc_start: 0.8920 (pp20) cc_final: 0.8674 (pp20) REVERT: C 320 HIS cc_start: 0.7866 (OUTLIER) cc_final: 0.7553 (p90) REVERT: D 140 MET cc_start: 0.6576 (mpm) cc_final: 0.4885 (ptt) REVERT: D 164 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8468 (mm) REVERT: D 177 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8416 (mtp85) REVERT: E 164 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8572 (mm) REVERT: E 184 TRP cc_start: 0.8072 (p-90) cc_final: 0.7758 (p-90) REVERT: E 245 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.6437 (t80) REVERT: E 250 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8494 (mmtm) REVERT: E 256 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8274 (mm-30) REVERT: E 281 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.7502 (t80) REVERT: G 247 ASP cc_start: 0.9084 (p0) cc_final: 0.8708 (p0) REVERT: G 334 ASP cc_start: 0.7620 (t0) cc_final: 0.7307 (t0) outliers start: 24 outliers final: 7 residues processed: 246 average time/residue: 0.6720 time to fit residues: 176.2887 Evaluate side-chains 244 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 245 TYR 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 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 E residue 281 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 106 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 211 ASN 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 = 0.123018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.076336 restraints weight = 17739.707| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.25 r_work: 0.2734 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13160 Z= 0.165 Angle : 0.593 11.637 17829 Z= 0.313 Chirality : 0.045 0.171 2037 Planarity : 0.004 0.069 2226 Dihedral : 9.868 172.493 1869 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.44 % Allowed : 15.30 % Favored : 83.26 % 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: 0.44 (0.21), residues: 1589 helix: 2.49 (0.19), residues: 693 sheet: -0.69 (0.36), residues: 217 loop : -1.82 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 271 TYR 0.016 0.002 TYR A 174 PHE 0.011 0.001 PHE D 209 TRP 0.030 0.002 TRP D 184 HIS 0.002 0.000 HIS C 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (13160) covalent geometry : angle 0.59303 / 0.31 (17829) hydrogen bonds : bond 0.03721 / 2.52 ( 707) hydrogen bonds : angle 4.14612 / 2.93 ( 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 247 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.6478 (mpt) cc_final: 0.5209 (mtp) REVERT: B 263 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8263 (mptm) REVERT: B 281 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7022 (t80) REVERT: C 184 TRP cc_start: 0.8009 (p-90) cc_final: 0.7772 (p-90) REVERT: C 245 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.7367 (t80) REVERT: C 320 HIS cc_start: 0.7830 (OUTLIER) cc_final: 0.6493 (p-80) REVERT: D 140 MET cc_start: 0.6728 (mpm) cc_final: 0.5003 (ptt) REVERT: D 177 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8375 (mtp85) REVERT: E 164 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8582 (mm) REVERT: E 184 TRP cc_start: 0.8076 (p-90) cc_final: 0.7825 (p-90) REVERT: E 245 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.6884 (t80) REVERT: E 250 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8527 (mmtm) REVERT: E 333 MET cc_start: 0.8055 (mpp) cc_final: 0.7819 (mmt) REVERT: G 205 LYS cc_start: 0.9151 (ttpt) cc_final: 0.8853 (ttpp) REVERT: G 247 ASP cc_start: 0.9194 (p0) cc_final: 0.8795 (p0) REVERT: G 334 ASP cc_start: 0.7586 (t0) cc_final: 0.7148 (t0) outliers start: 20 outliers final: 7 residues processed: 240 average time/residue: 0.6222 time to fit residues: 159.9122 Evaluate side-chains 237 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 222 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 245 TYR 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 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 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: 1.9990 chunk 95 optimal weight: 0.0770 chunk 82 optimal weight: 0.9980 chunk 94 optimal weight: 0.0770 chunk 111 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.124494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.078549 restraints weight = 18132.639| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.27 r_work: 0.2788 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13160 Z= 0.115 Angle : 0.560 9.798 17829 Z= 0.293 Chirality : 0.043 0.195 2037 Planarity : 0.004 0.063 2226 Dihedral : 9.585 171.478 1869 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.37 % Allowed : 15.37 % Favored : 83.26 % 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: 0.50 (0.22), residues: 1589 helix: 2.57 (0.19), residues: 693 sheet: -0.70 (0.36), residues: 217 loop : -1.82 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 271 TYR 0.016 0.001 TYR G 174 PHE 0.015 0.001 PHE F 324 TRP 0.027 0.002 TRP G 184 HIS 0.002 0.000 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (13160) covalent geometry : angle 0.55962 / 0.29 (17829) hydrogen bonds : bond 0.03333 / 2.26 ( 707) hydrogen bonds : angle 4.05860 / 2.87 ( 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 257 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 238 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.6545 (mpt) cc_final: 0.5027 (mtp) REVERT: A 222 SER cc_start: 0.9236 (m) cc_final: 0.8634 (p) REVERT: B 222 SER cc_start: 0.8468 (p) cc_final: 0.8246 (p) REVERT: B 263 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8413 (mptm) REVERT: B 281 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7016 (t80) REVERT: B 333 MET cc_start: 0.7846 (mmm) cc_final: 0.7598 (mmm) REVERT: C 246 GLU cc_start: 0.8920 (pp20) cc_final: 0.8662 (pp20) REVERT: C 301 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8287 (pt0) REVERT: C 320 HIS cc_start: 0.7907 (OUTLIER) cc_final: 0.7661 (p90) REVERT: C 334 ASP cc_start: 0.7153 (t0) cc_final: 0.6835 (t70) REVERT: D 140 MET cc_start: 0.6752 (mpm) cc_final: 0.5019 (ptt) REVERT: D 164 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8515 (mm) REVERT: D 177 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8484 (mtp85) REVERT: E 164 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8674 (mm) REVERT: E 184 TRP cc_start: 0.8149 (p-90) cc_final: 0.7895 (p-90) REVERT: E 245 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.6763 (t80) REVERT: E 250 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8714 (mmtm) REVERT: E 256 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8435 (mm-30) REVERT: F 118 MET cc_start: 0.3641 (OUTLIER) cc_final: 0.3058 (ptp) REVERT: G 140 MET cc_start: 0.5480 (pmm) cc_final: 0.3618 (ptt) REVERT: G 247 ASP cc_start: 0.9030 (p0) cc_final: 0.8672 (p0) REVERT: G 334 ASP cc_start: 0.7678 (t0) cc_final: 0.7302 (t0) outliers start: 19 outliers final: 6 residues processed: 249 average time/residue: 0.6646 time to fit residues: 177.3203 Evaluate side-chains 242 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 227 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 46 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 78 optimal weight: 0.3980 chunk 137 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 211 ASN 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 = 0.122334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.075716 restraints weight = 18080.206| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.27 r_work: 0.2742 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13160 Z= 0.159 Angle : 0.596 11.510 17829 Z= 0.314 Chirality : 0.045 0.223 2037 Planarity : 0.005 0.070 2226 Dihedral : 9.547 171.100 1869 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.52 % Allowed : 15.66 % Favored : 82.83 % 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: 0.47 (0.21), residues: 1589 helix: 2.55 (0.19), residues: 693 sheet: -0.67 (0.36), residues: 217 loop : -1.85 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 271 TYR 0.021 0.002 TYR C 174 PHE 0.011 0.001 PHE D 209 TRP 0.028 0.002 TRP G 184 HIS 0.002 0.000 HIS C 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (13160) covalent geometry : angle 0.59583 / 0.31 (17829) hydrogen bonds : bond 0.03710 / 2.51 ( 707) hydrogen bonds : angle 4.12076 / 2.91 ( 1998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5614.71 seconds wall clock time: 95 minutes 54.72 seconds (5754.72 seconds total)