Starting phenix.real_space_refine on Thu Jul 31 04:43:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n4t_24177/07_2025/7n4t_24177.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n4t_24177/07_2025/7n4t_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_24177/07_2025/7n4t_24177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n4t_24177/07_2025/7n4t_24177.map" model { file = "/net/cci-nas-00/data/ceres_data/7n4t_24177/07_2025/7n4t_24177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n4t_24177/07_2025/7n4t_24177.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.40, per 1000 atoms: 0.65 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: 3.49 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.54 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: 4.09 Time building geometry restraints manager: 3.92 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: 0.02 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: 63.440 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.580 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:92.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 189.870 ------------------------------------------------------------------------------- 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 : 7.06 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (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 TRP 0.013 0.001 TRP G 184 HIS 0.002 0.000 HIS G 137 PHE 0.018 0.001 PHE A 281 TYR 0.022 0.002 TYR A 245 ARG 0.011 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.12842 ( 707) hydrogen bonds : angle 5.87704 ( 1998) covalent geometry : bond 0.00447 (13160) covalent geometry : angle 0.89587 (17829) *********************** 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 : 1.478 Fit side-chains revert: symmetry clash REVERT: C 118 MET cc_start: 0.6519 (ttt) cc_final: 0.5446 (ptp) 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: 1.8580 time to fit residues: 580.4410 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 : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 73 optimal weight: 0.2980 chunk 89 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.123303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.076441 restraints weight = 17656.145| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.36 r_work: 0.2751 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13160 Z= 0.187 Angle : 0.599 6.491 17829 Z= 0.324 Chirality : 0.046 0.172 2037 Planarity : 0.005 0.074 2226 Dihedral : 21.090 176.483 1939 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.09 % Allowed : 9.38 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1589 helix: 2.31 (0.19), residues: 686 sheet: -1.07 (0.33), residues: 259 loop : -1.54 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 184 HIS 0.003 0.000 HIS G 137 PHE 0.021 0.002 PHE G 324 TYR 0.024 0.002 TYR E 174 ARG 0.005 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 707) hydrogen bonds : angle 4.61326 ( 1998) covalent geometry : bond 0.00427 (13160) covalent geometry : angle 0.59906 (17829) *********************** 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 275 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 246 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 263 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8472 (mptm) REVERT: B 333 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8059 (mmm) REVERT: C 118 MET cc_start: 0.6490 (ttt) cc_final: 0.5336 (ptt) REVERT: C 333 MET cc_start: 0.7408 (mmm) cc_final: 0.6940 (mmm) REVERT: E 184 TRP cc_start: 0.8233 (p-90) cc_final: 0.7973 (p-90) REVERT: E 250 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8740 (mmtm) REVERT: E 334 ASP cc_start: 0.7382 (t0) cc_final: 0.7107 (t70) REVERT: F 118 MET cc_start: 0.4168 (OUTLIER) cc_final: 0.3732 (ptp) REVERT: F 205 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.9112 (ttmt) REVERT: F 263 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8246 (mptm) REVERT: G 247 ASP cc_start: 0.9108 (p0) cc_final: 0.8673 (p0) REVERT: G 263 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8513 (mptm) outliers start: 29 outliers final: 6 residues processed: 252 average time/residue: 1.5609 time to fit residues: 421.8533 Evaluate side-chains 248 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 235 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain D residue 247 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 164 LEU 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 94 optimal weight: 0.3980 chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 30.0000 chunk 3 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 119 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.125226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.078778 restraints weight = 17965.167| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.38 r_work: 0.2799 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13160 Z= 0.123 Angle : 0.542 6.703 17829 Z= 0.289 Chirality : 0.043 0.156 2037 Planarity : 0.004 0.067 2226 Dihedral : 19.958 170.109 1939 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.02 % Allowed : 10.10 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1589 helix: 2.42 (0.20), residues: 686 sheet: -1.11 (0.33), residues: 259 loop : -1.56 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 184 HIS 0.002 0.000 HIS A 320 PHE 0.012 0.001 PHE G 324 TYR 0.030 0.001 TYR F 245 ARG 0.007 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 707) hydrogen bonds : angle 4.34651 ( 1998) covalent geometry : bond 0.00259 (13160) covalent geometry : angle 0.54166 (17829) *********************** 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 280 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 252 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 263 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8445 (mptm) REVERT: B 264 ASN cc_start: 0.9244 (m-40) cc_final: 0.8950 (m-40) REVERT: C 320 HIS cc_start: 0.7970 (OUTLIER) cc_final: 0.6887 (p-80) REVERT: D 193 GLU cc_start: 0.9142 (tt0) cc_final: 0.8927 (tt0) REVERT: D 247 ASP cc_start: 0.8367 (p0) cc_final: 0.7712 (m-30) REVERT: E 184 TRP cc_start: 0.8160 (p-90) cc_final: 0.7845 (p-90) REVERT: E 245 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.6745 (t80) REVERT: E 250 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8690 (mmtm) REVERT: F 118 MET cc_start: 0.4102 (OUTLIER) cc_final: 0.3503 (ptp) REVERT: F 205 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.9111 (ttmt) REVERT: F 334 ASP cc_start: 0.7755 (t0) cc_final: 0.7528 (t0) REVERT: G 247 ASP cc_start: 0.9022 (p0) cc_final: 0.8569 (p0) outliers start: 28 outliers final: 7 residues processed: 260 average time/residue: 1.7112 time to fit residues: 477.0924 Evaluate side-chains 250 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 237 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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 232 MET 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 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 17 optimal weight: 0.0970 chunk 102 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 129 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 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 = 0.3661 r_free = 0.3661 target = 0.125136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.078995 restraints weight = 17781.011| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.38 r_work: 0.2810 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13160 Z= 0.116 Angle : 0.525 6.807 17829 Z= 0.279 Chirality : 0.043 0.148 2037 Planarity : 0.004 0.063 2226 Dihedral : 19.148 176.776 1939 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.09 % Allowed : 10.68 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.22), residues: 1589 helix: 2.46 (0.19), residues: 693 sheet: -1.10 (0.33), residues: 259 loop : -1.55 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 184 HIS 0.016 0.001 HIS E 137 PHE 0.011 0.001 PHE F 324 TYR 0.033 0.001 TYR F 245 ARG 0.008 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 707) hydrogen bonds : angle 4.19641 ( 1998) covalent geometry : bond 0.00246 (13160) covalent geometry : angle 0.52456 (17829) *********************** 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 269 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 245 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.8728 (m-80) REVERT: B 263 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8448 (mptm) REVERT: B 264 ASN cc_start: 0.9215 (m-40) cc_final: 0.8915 (m-40) REVERT: B 281 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7035 (t80) REVERT: C 320 HIS cc_start: 0.7947 (OUTLIER) cc_final: 0.6829 (p-80) REVERT: D 193 GLU cc_start: 0.9147 (tt0) cc_final: 0.8944 (tt0) REVERT: E 184 TRP cc_start: 0.8152 (p-90) cc_final: 0.7851 (p-90) REVERT: E 245 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.6691 (t80) REVERT: E 250 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8695 (mmtm) REVERT: F 118 MET cc_start: 0.3872 (OUTLIER) cc_final: 0.3342 (ptp) REVERT: F 245 TYR cc_start: 0.6812 (t80) cc_final: 0.6475 (t80) REVERT: F 263 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8263 (mptm) REVERT: F 333 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.8024 (tpp) REVERT: G 247 ASP cc_start: 0.9032 (p0) cc_final: 0.8582 (p0) outliers start: 29 outliers final: 9 residues processed: 253 average time/residue: 1.6901 time to fit residues: 458.5158 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 : 1.498 ------------------------------------------------------------------------------- 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 245 TYR 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 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 F residue 263 LYS Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain G residue 196 VAL 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 44 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.123124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.076241 restraints weight = 17833.086| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.34 r_work: 0.2749 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13160 Z= 0.168 Angle : 0.579 11.029 17829 Z= 0.309 Chirality : 0.045 0.163 2037 Planarity : 0.005 0.071 2226 Dihedral : 18.721 177.414 1939 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.09 % Allowed : 11.47 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1589 helix: 2.43 (0.19), residues: 693 sheet: -0.66 (0.36), residues: 217 loop : -1.72 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 184 HIS 0.003 0.001 HIS A 320 PHE 0.014 0.001 PHE G 324 TYR 0.015 0.002 TYR F 245 ARG 0.015 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 707) hydrogen bonds : angle 4.23525 ( 1998) covalent geometry : bond 0.00384 (13160) covalent geometry : angle 0.57889 (17829) *********************** 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: 29 poor density : 229 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 ASN cc_start: 0.9149 (m-40) cc_final: 0.8844 (m-40) REVERT: B 281 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7182 (t80) REVERT: C 320 HIS cc_start: 0.7826 (OUTLIER) cc_final: 0.6591 (p-80) REVERT: D 193 GLU cc_start: 0.9124 (tt0) cc_final: 0.8868 (tt0) REVERT: E 164 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8642 (mm) REVERT: E 184 TRP cc_start: 0.8103 (p-90) cc_final: 0.7898 (p-90) REVERT: E 245 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.6633 (t80) REVERT: E 250 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8578 (mmtm) REVERT: F 118 MET cc_start: 0.3833 (OUTLIER) cc_final: 0.3308 (ptp) REVERT: F 140 MET cc_start: 0.6395 (pmm) cc_final: 0.6137 (pmm) REVERT: F 263 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8116 (mptm) REVERT: G 247 ASP cc_start: 0.9195 (p0) cc_final: 0.8770 (p0) outliers start: 29 outliers final: 9 residues processed: 239 average time/residue: 1.6663 time to fit residues: 425.5907 Evaluate side-chains 242 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 226 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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 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 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 F residue 333 MET 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 117 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.121715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.074392 restraints weight = 18185.671| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.28 r_work: 0.2713 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2189 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= 0.202 Angle : 0.613 11.865 17829 Z= 0.327 Chirality : 0.046 0.178 2037 Planarity : 0.005 0.076 2226 Dihedral : 18.361 177.725 1939 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.31 % Allowed : 12.48 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1589 helix: 2.40 (0.19), residues: 693 sheet: -0.70 (0.35), residues: 217 loop : -1.75 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP G 184 HIS 0.002 0.000 HIS C 320 PHE 0.017 0.002 PHE D 209 TYR 0.023 0.002 TYR E 174 ARG 0.015 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.04029 ( 707) hydrogen bonds : angle 4.25676 ( 1998) covalent geometry : bond 0.00471 (13160) covalent geometry : angle 0.61327 (17829) *********************** 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 265 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 1.593 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: 0.6804 (mpt) cc_final: 0.6485 (mpp) REVERT: B 264 ASN cc_start: 0.9272 (m-40) cc_final: 0.8947 (m-40) REVERT: B 281 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7119 (t80) REVERT: C 320 HIS cc_start: 0.7992 (OUTLIER) cc_final: 0.6732 (p-80) REVERT: E 245 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.7031 (t80) REVERT: E 250 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8706 (mmtm) REVERT: F 118 MET cc_start: 0.3722 (OUTLIER) cc_final: 0.3208 (ptp) REVERT: G 247 ASP cc_start: 0.9231 (p0) cc_final: 0.8804 (p0) REVERT: G 263 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8485 (mptm) outliers start: 32 outliers final: 9 residues processed: 244 average time/residue: 2.1578 time to fit residues: 564.3761 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 : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU 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 D residue 158 MET 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 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 127 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 59 optimal weight: 0.4980 chunk 149 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.123124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.076248 restraints weight = 17605.382| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.25 r_work: 0.2733 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13160 Z= 0.162 Angle : 0.584 12.240 17829 Z= 0.310 Chirality : 0.045 0.156 2037 Planarity : 0.005 0.072 2226 Dihedral : 18.056 179.492 1939 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.16 % Allowed : 13.64 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1589 helix: 2.46 (0.19), residues: 693 sheet: -0.70 (0.35), residues: 217 loop : -1.77 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 184 HIS 0.003 0.000 HIS A 320 PHE 0.012 0.001 PHE D 209 TYR 0.014 0.002 TYR B 291 ARG 0.016 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 707) hydrogen bonds : angle 4.18474 ( 1998) covalent geometry : bond 0.00368 (13160) covalent geometry : angle 0.58430 (17829) *********************** 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 260 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 MET cc_start: 0.8460 (mmm) cc_final: 0.8240 (mmm) REVERT: B 140 MET cc_start: 0.7281 (mpt) cc_final: 0.7044 (mpp) REVERT: B 263 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8207 (mptm) REVERT: B 264 ASN cc_start: 0.9121 (m-40) cc_final: 0.8801 (m-40) REVERT: B 281 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.6998 (t80) REVERT: C 246 GLU cc_start: 0.8918 (pp20) cc_final: 0.8687 (pp20) REVERT: C 320 HIS cc_start: 0.7898 (OUTLIER) cc_final: 0.6523 (p-80) REVERT: D 140 MET cc_start: 0.6794 (mpm) cc_final: 0.4993 (ptt) REVERT: D 177 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8382 (mtp85) REVERT: D 333 MET cc_start: 0.8580 (mpp) cc_final: 0.8266 (mmt) REVERT: E 245 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.6933 (t80) REVERT: E 250 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8511 (mmtm) REVERT: F 118 MET cc_start: 0.3586 (OUTLIER) cc_final: 0.3129 (ptp) REVERT: F 140 MET cc_start: 0.6216 (pmm) cc_final: 0.5972 (pmm) REVERT: G 247 ASP cc_start: 0.9208 (p0) cc_final: 0.8739 (p0) REVERT: G 263 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8300 (mptm) outliers start: 30 outliers final: 6 residues processed: 243 average time/residue: 1.6324 time to fit residues: 425.7908 Evaluate side-chains 239 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 225 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 177 ARG 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 Chi-restraints excluded: chain G residue 263 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.122934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.075893 restraints weight = 17701.605| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.26 r_work: 0.2730 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2303 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= 0.165 Angle : 0.589 13.227 17829 Z= 0.313 Chirality : 0.045 0.159 2037 Planarity : 0.005 0.073 2226 Dihedral : 17.877 179.471 1939 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.73 % Allowed : 14.72 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1589 helix: 2.46 (0.19), residues: 693 sheet: -0.73 (0.35), residues: 217 loop : -1.80 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 184 HIS 0.002 0.000 HIS C 320 PHE 0.013 0.001 PHE D 209 TYR 0.016 0.002 TYR A 174 ARG 0.017 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 707) hydrogen bonds : angle 4.17206 ( 1998) covalent geometry : bond 0.00376 (13160) covalent geometry : angle 0.58934 (17829) *********************** 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 253 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 MET cc_start: 0.8308 (mmm) cc_final: 0.8065 (mmm) REVERT: B 263 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8204 (mptm) REVERT: B 264 ASN cc_start: 0.9122 (m-40) cc_final: 0.8798 (m-40) REVERT: B 281 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7001 (t80) REVERT: C 246 GLU cc_start: 0.8927 (pp20) cc_final: 0.8664 (pp20) REVERT: C 320 HIS cc_start: 0.7895 (OUTLIER) cc_final: 0.6504 (p-80) REVERT: D 177 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8384 (mtp85) REVERT: E 245 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.7009 (t80) REVERT: E 250 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8511 (mmtm) REVERT: E 256 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8260 (mm-30) REVERT: F 118 MET cc_start: 0.3591 (OUTLIER) cc_final: 0.3116 (ptp) REVERT: G 247 ASP cc_start: 0.9180 (p0) cc_final: 0.8736 (p0) REVERT: G 263 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8308 (mptm) outliers start: 24 outliers final: 6 residues processed: 241 average time/residue: 1.5924 time to fit residues: 410.3019 Evaluate side-chains 240 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 D residue 177 ARG 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 Chi-restraints excluded: chain G residue 263 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 45 optimal weight: 7.9990 chunk 35 optimal weight: 0.0370 chunk 46 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.124319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.078068 restraints weight = 17827.438| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.27 r_work: 0.2779 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2371 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= 0.120 Angle : 0.570 12.780 17829 Z= 0.296 Chirality : 0.043 0.180 2037 Planarity : 0.004 0.077 2226 Dihedral : 17.586 179.759 1939 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.37 % Allowed : 15.22 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1589 helix: 2.55 (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 TRP 0.023 0.002 TRP G 184 HIS 0.002 0.000 HIS A 137 PHE 0.014 0.001 PHE F 324 TYR 0.016 0.001 TYR D 174 ARG 0.018 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 707) hydrogen bonds : angle 4.07695 ( 1998) covalent geometry : bond 0.00257 (13160) covalent geometry : angle 0.57007 (17829) *********************** 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 262 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 243 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.6577 (mpt) cc_final: 0.5162 (mtp) REVERT: B 140 MET cc_start: 0.7065 (mpt) cc_final: 0.6838 (mpp) REVERT: B 222 SER cc_start: 0.8474 (p) cc_final: 0.8250 (p) REVERT: B 263 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8456 (mptm) REVERT: B 281 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7036 (t80) REVERT: C 320 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.7575 (p90) REVERT: D 140 MET cc_start: 0.6774 (mpm) cc_final: 0.5235 (ptt) REVERT: D 164 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8526 (mm) REVERT: D 177 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8417 (mtp85) REVERT: E 164 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8629 (mm) REVERT: E 245 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.6421 (t80) REVERT: E 250 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8638 (mmtm) REVERT: E 256 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8410 (mm-30) REVERT: E 281 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.7385 (t80) REVERT: F 118 MET cc_start: 0.3725 (OUTLIER) cc_final: 0.3138 (ptp) REVERT: G 247 ASP cc_start: 0.9044 (p0) cc_final: 0.8663 (p0) outliers start: 19 outliers final: 6 residues processed: 255 average time/residue: 1.5680 time to fit residues: 428.4184 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 : 1.325 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 21 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.121867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.074868 restraints weight = 17924.476| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.29 r_work: 0.2719 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13160 Z= 0.184 Angle : 0.616 11.485 17829 Z= 0.326 Chirality : 0.046 0.232 2037 Planarity : 0.005 0.072 2226 Dihedral : 17.503 179.249 1939 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.23 % Allowed : 16.09 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1589 helix: 2.48 (0.19), residues: 693 sheet: -0.71 (0.35), residues: 217 loop : -1.86 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 184 HIS 0.002 0.000 HIS C 320 PHE 0.014 0.001 PHE D 209 TYR 0.017 0.002 TYR A 174 ARG 0.017 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 707) hydrogen bonds : angle 4.15264 ( 1998) covalent geometry : bond 0.00427 (13160) covalent geometry : angle 0.61634 (17829) ********************** 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 244 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.6549 (mpt) cc_final: 0.5196 (ptp) REVERT: B 140 MET cc_start: 0.7241 (mpt) cc_final: 0.7009 (mpp) REVERT: B 263 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8441 (mptm) REVERT: B 281 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7088 (t80) REVERT: C 246 GLU cc_start: 0.8912 (pp20) cc_final: 0.8667 (pp20) REVERT: C 320 HIS cc_start: 0.7995 (OUTLIER) cc_final: 0.6578 (p-80) REVERT: D 140 MET cc_start: 0.6810 (mpm) cc_final: 0.5217 (ptt) REVERT: E 164 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8735 (mm) REVERT: E 245 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.7135 (t80) REVERT: E 250 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8677 (mmtm) REVERT: F 118 MET cc_start: 0.3635 (OUTLIER) cc_final: 0.3053 (ptp) REVERT: G 140 MET cc_start: 0.5532 (pmm) cc_final: 0.3596 (ptt) REVERT: G 247 ASP cc_start: 0.9206 (p0) cc_final: 0.8752 (p0) outliers start: 17 outliers final: 7 residues processed: 238 average time/residue: 1.5350 time to fit residues: 391.2168 Evaluate side-chains 242 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 228 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU 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 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 100 optimal weight: 3.9990 chunk 9 optimal weight: 0.0570 chunk 4 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.122961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.076204 restraints weight = 17941.300| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.30 r_work: 0.2759 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13160 Z= 0.133 Angle : 0.594 13.965 17829 Z= 0.308 Chirality : 0.044 0.235 2037 Planarity : 0.004 0.071 2226 Dihedral : 17.301 178.326 1939 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.15 % Allowed : 16.16 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.21), residues: 1589 helix: 2.56 (0.19), residues: 693 sheet: -0.71 (0.35), residues: 217 loop : -1.85 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 184 HIS 0.002 0.000 HIS A 320 PHE 0.013 0.001 PHE F 324 TYR 0.017 0.002 TYR D 174 ARG 0.017 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 707) hydrogen bonds : angle 4.08575 ( 1998) covalent geometry : bond 0.00293 (13160) covalent geometry : angle 0.59432 (17829) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14439.97 seconds wall clock time: 253 minutes 34.30 seconds (15214.30 seconds total)