Starting phenix.real_space_refine on Mon Dec 30 12:30:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n4t_24177/12_2024/7n4t_24177.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n4t_24177/12_2024/7n4t_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_24177/12_2024/7n4t_24177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n4t_24177/12_2024/7n4t_24177.map" model { file = "/net/cci-nas-00/data/ceres_data/7n4t_24177/12_2024/7n4t_24177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n4t_24177/12_2024/7n4t_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-5532/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: 7.94, per 1000 atoms: 0.62 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: 3.61 Conformation dependent library (CDL) restraints added in 1.7 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: 1.34 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: 3.92 Time building geometry restraints manager: 4.06 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: 0.00 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: 1.480 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: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.800 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.600 ------------------------------------------------------------------------------- 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= 0.292 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 *********************** 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 : 1.464 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: 1.5743 time to fit residues: 492.6200 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 : 1.452 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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= 0.280 Angle : 0.599 6.482 17829 Z= 0.324 Chirality : 0.046 0.172 2037 Planarity : 0.005 0.074 2226 Dihedral : 21.088 176.436 1939 Min Nonbonded Distance : 2.407 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 *********************** 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 : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 263 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8379 (mptm) REVERT: C 118 MET cc_start: 0.6604 (ttt) cc_final: 0.5575 (ptt) REVERT: C 333 MET cc_start: 0.6400 (mmm) cc_final: 0.6080 (mmm) REVERT: D 113 THR cc_start: 0.5267 (OUTLIER) cc_final: 0.5005 (m) REVERT: E 250 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8499 (mmtm) REVERT: F 118 MET cc_start: 0.4598 (OUTLIER) cc_final: 0.3781 (ptp) REVERT: F 205 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8913 (ttmt) REVERT: F 263 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8092 (mptm) REVERT: G 247 ASP cc_start: 0.8434 (p0) cc_final: 0.8094 (p0) REVERT: G 263 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8547 (mptm) outliers start: 29 outliers final: 6 residues processed: 252 average time/residue: 1.6317 time to fit residues: 440.9535 Evaluate side-chains 247 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 234 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain D residue 113 THR 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 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 140 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1740 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= 0.212 Angle : 0.565 6.662 17829 Z= 0.302 Chirality : 0.044 0.162 2037 Planarity : 0.004 0.071 2226 Dihedral : 20.055 170.011 1939 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.16 % Allowed : 10.03 % Favored : 87.81 % 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: 0.38 (0.21), residues: 1589 helix: 2.39 (0.19), residues: 686 sheet: -1.14 (0.33), residues: 259 loop : -1.58 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 184 HIS 0.002 0.000 HIS A 320 PHE 0.014 0.001 PHE G 324 TYR 0.028 0.002 TYR F 245 ARG 0.007 0.000 ARG A 271 *********************** 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 278 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 248 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 263 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8390 (mptm) REVERT: B 264 ASN cc_start: 0.8837 (m-40) cc_final: 0.8583 (m-40) REVERT: B 281 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7077 (t80) REVERT: C 320 HIS cc_start: 0.7501 (OUTLIER) cc_final: 0.6501 (p-80) REVERT: E 245 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.6486 (t80) REVERT: E 250 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8460 (mmtm) REVERT: F 118 MET cc_start: 0.4632 (OUTLIER) cc_final: 0.3629 (ptp) REVERT: G 247 ASP cc_start: 0.8470 (p0) cc_final: 0.8061 (p0) REVERT: G 263 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8550 (mptm) outliers start: 30 outliers final: 9 residues processed: 257 average time/residue: 1.5456 time to fit residues: 426.1996 Evaluate side-chains 251 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 235 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET 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 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 C residue 333 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 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 138 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 72 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 148 optimal weight: 0.4980 chunk 73 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1975 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= 0.198 Angle : 0.553 7.377 17829 Z= 0.295 Chirality : 0.044 0.158 2037 Planarity : 0.004 0.069 2226 Dihedral : 19.268 176.090 1939 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.38 % Allowed : 10.39 % 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: 0.41 (0.22), residues: 1589 helix: 2.44 (0.19), residues: 686 sheet: -1.15 (0.33), residues: 259 loop : -1.59 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 184 HIS 0.012 0.001 HIS E 137 PHE 0.012 0.001 PHE C 281 TYR 0.036 0.002 TYR F 245 ARG 0.009 0.000 ARG A 271 *********************** 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: 33 poor density : 236 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 263 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8390 (mptm) REVERT: B 264 ASN cc_start: 0.8818 (m-40) cc_final: 0.8598 (m-40) REVERT: B 281 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.6950 (t80) REVERT: C 320 HIS cc_start: 0.7506 (OUTLIER) cc_final: 0.6490 (p-80) REVERT: D 118 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6834 (ttp) REVERT: E 245 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.6468 (t80) REVERT: E 250 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8436 (mmtm) REVERT: F 118 MET cc_start: 0.4164 (OUTLIER) cc_final: 0.3187 (ptp) REVERT: G 247 ASP cc_start: 0.8466 (p0) cc_final: 0.8094 (p0) outliers start: 33 outliers final: 8 residues processed: 249 average time/residue: 1.6128 time to fit residues: 429.5429 Evaluate side-chains 243 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 228 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain D residue 118 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 E residue 281 PHE Chi-restraints excluded: chain F residue 118 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 123 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 chunk 110 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 76 optimal weight: 0.0010 chunk 133 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13160 Z= 0.216 Angle : 0.571 11.632 17829 Z= 0.301 Chirality : 0.044 0.157 2037 Planarity : 0.004 0.070 2226 Dihedral : 18.699 176.936 1939 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.02 % Allowed : 11.83 % Favored : 86.15 % 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: 0.44 (0.21), residues: 1589 helix: 2.46 (0.19), residues: 693 sheet: -0.69 (0.36), residues: 217 loop : -1.79 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 184 HIS 0.008 0.001 HIS E 137 PHE 0.011 0.001 PHE D 209 TYR 0.014 0.002 TYR B 291 ARG 0.014 0.000 ARG A 271 *********************** 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: 28 poor density : 230 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 ASN cc_start: 0.8828 (m-40) cc_final: 0.8587 (m-40) REVERT: B 281 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7132 (t80) REVERT: C 320 HIS cc_start: 0.7524 (OUTLIER) cc_final: 0.6511 (p-80) REVERT: D 118 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6862 (ttp) REVERT: E 245 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.6488 (t80) REVERT: E 250 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8430 (mmtm) REVERT: F 118 MET cc_start: 0.4063 (OUTLIER) cc_final: 0.3211 (ptp) REVERT: F 140 MET cc_start: 0.5804 (pmm) cc_final: 0.5573 (pmm) REVERT: F 263 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8201 (mptm) REVERT: G 247 ASP cc_start: 0.8511 (p0) cc_final: 0.8153 (p0) outliers start: 28 outliers final: 9 residues processed: 243 average time/residue: 1.7397 time to fit residues: 451.3825 Evaluate side-chains 246 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 230 time to evaluate : 1.473 ------------------------------------------------------------------------------- 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 118 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 F residue 158 MET Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 7.9990 chunk 134 optimal weight: 20.0000 chunk 29 optimal weight: 0.0670 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 149 optimal weight: 0.0970 chunk 123 optimal weight: 0.0770 chunk 68 optimal weight: 10.0000 chunk 12 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2249 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= 0.137 Angle : 0.541 11.647 17829 Z= 0.277 Chirality : 0.042 0.136 2037 Planarity : 0.004 0.061 2226 Dihedral : 18.053 177.825 1939 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.95 % Allowed : 12.77 % Favored : 85.28 % 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: 0.55 (0.22), residues: 1589 helix: 2.59 (0.20), residues: 693 sheet: -0.66 (0.36), residues: 217 loop : -1.77 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 184 HIS 0.004 0.000 HIS E 137 PHE 0.016 0.001 PHE F 324 TYR 0.015 0.001 TYR A 174 ARG 0.011 0.000 ARG A 271 *********************** 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 273 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 246 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 SER cc_start: 0.8915 (m) cc_final: 0.8665 (p) REVERT: B 245 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.7103 (t80) REVERT: B 263 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8399 (mptm) REVERT: D 118 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6802 (ttp) REVERT: D 140 MET cc_start: 0.6876 (mpm) cc_final: 0.5619 (ptt) REVERT: D 164 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8655 (mm) REVERT: D 222 SER cc_start: 0.8694 (m) cc_final: 0.8409 (p) REVERT: E 164 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8810 (mm) REVERT: E 245 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.6141 (t80) REVERT: E 250 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8395 (mmtm) REVERT: E 281 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.7150 (t80) REVERT: F 118 MET cc_start: 0.4032 (OUTLIER) cc_final: 0.3166 (ptt) REVERT: G 247 ASP cc_start: 0.8364 (p0) cc_final: 0.8037 (p0) outliers start: 27 outliers final: 6 residues processed: 260 average time/residue: 1.5657 time to fit residues: 436.0288 Evaluate side-chains 250 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 235 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 323 ASP Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 164 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 84 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 148 optimal weight: 0.4980 chunk 92 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 320 HIS E 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13160 Z= 0.211 Angle : 0.568 9.693 17829 Z= 0.299 Chirality : 0.044 0.151 2037 Planarity : 0.004 0.065 2226 Dihedral : 17.902 179.141 1939 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.80 % Allowed : 13.42 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.22), residues: 1589 helix: 2.52 (0.19), residues: 693 sheet: -0.65 (0.36), residues: 217 loop : -1.80 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 184 HIS 0.005 0.001 HIS E 137 PHE 0.011 0.001 PHE D 209 TYR 0.022 0.002 TYR E 174 ARG 0.013 0.000 ARG A 271 *********************** 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 259 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 234 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 SER cc_start: 0.9004 (m) cc_final: 0.8778 (p) REVERT: B 263 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8432 (mptm) REVERT: B 281 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7179 (t80) REVERT: C 320 HIS cc_start: 0.7515 (OUTLIER) cc_final: 0.6184 (p-80) REVERT: D 118 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6805 (ttp) REVERT: D 140 MET cc_start: 0.6953 (mpm) cc_final: 0.5777 (ptt) REVERT: D 177 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7738 (mtp85) REVERT: E 164 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8822 (mm) REVERT: E 245 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.6475 (t80) REVERT: E 250 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8415 (mmtm) REVERT: F 118 MET cc_start: 0.3892 (OUTLIER) cc_final: 0.3022 (ptp) REVERT: G 247 ASP cc_start: 0.8447 (p0) cc_final: 0.8160 (p0) outliers start: 25 outliers final: 7 residues processed: 248 average time/residue: 1.6295 time to fit residues: 431.9942 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 : 1.445 ------------------------------------------------------------------------------- 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 118 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 F residue 118 MET Chi-restraints excluded: chain F 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 29 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 101 optimal weight: 0.0570 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 overall best weight: 0.9104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 137 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2344 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= 0.191 Angle : 0.571 12.496 17829 Z= 0.299 Chirality : 0.044 0.152 2037 Planarity : 0.004 0.079 2226 Dihedral : 17.817 179.846 1939 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.73 % Allowed : 14.50 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1589 helix: 2.54 (0.19), residues: 693 sheet: -0.65 (0.36), residues: 217 loop : -1.80 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 184 HIS 0.005 0.001 HIS E 137 PHE 0.012 0.001 PHE F 324 TYR 0.016 0.002 TYR A 174 ARG 0.018 0.000 ARG A 271 *********************** 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 258 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 234 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 SER cc_start: 0.8996 (m) cc_final: 0.8764 (p) REVERT: B 263 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8424 (mptm) REVERT: B 281 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7065 (t80) REVERT: C 320 HIS cc_start: 0.7517 (OUTLIER) cc_final: 0.5901 (p90) REVERT: D 118 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6782 (ttp) REVERT: D 140 MET cc_start: 0.7009 (mpm) cc_final: 0.5728 (ptt) REVERT: D 164 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8679 (mm) REVERT: D 177 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7720 (mtp85) REVERT: E 164 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8805 (mm) REVERT: E 245 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.6483 (t80) REVERT: E 250 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8418 (mmtm) REVERT: F 118 MET cc_start: 0.3898 (OUTLIER) cc_final: 0.3019 (ptp) outliers start: 24 outliers final: 6 residues processed: 246 average time/residue: 1.6279 time to fit residues: 428.3669 Evaluate side-chains 251 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 235 time to evaluate : 1.469 ------------------------------------------------------------------------------- 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 B residue 301 GLU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain D residue 118 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 60 optimal weight: 0.0770 chunk 108 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 320 HIS E 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13160 Z= 0.154 Angle : 0.555 11.077 17829 Z= 0.287 Chirality : 0.043 0.178 2037 Planarity : 0.004 0.062 2226 Dihedral : 17.569 179.021 1939 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.52 % Allowed : 15.01 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.22), residues: 1589 helix: 2.60 (0.19), residues: 693 sheet: -0.66 (0.36), residues: 217 loop : -1.79 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 184 HIS 0.003 0.000 HIS E 137 PHE 0.014 0.001 PHE F 324 TYR 0.015 0.001 TYR G 174 ARG 0.012 0.000 ARG A 271 *********************** 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 267 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 246 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.6278 (mpt) cc_final: 0.5227 (mtp) REVERT: A 222 SER cc_start: 0.8964 (m) cc_final: 0.8739 (p) REVERT: B 263 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8417 (mptm) REVERT: C 172 MET cc_start: 0.8395 (tpt) cc_final: 0.8114 (mmm) REVERT: C 320 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.6081 (p-80) REVERT: D 164 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8651 (mm) REVERT: E 164 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8777 (mm) REVERT: E 245 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.6175 (t80) REVERT: E 250 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8412 (mmtm) REVERT: E 281 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7075 (t80) REVERT: F 118 MET cc_start: 0.3908 (OUTLIER) cc_final: 0.2954 (ptp) REVERT: G 247 ASP cc_start: 0.8375 (p0) cc_final: 0.8082 (p0) outliers start: 21 outliers final: 5 residues processed: 258 average time/residue: 1.6049 time to fit residues: 443.1513 Evaluate side-chains 253 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 240 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 164 LEU 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 146 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 137 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 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 0.030 13160 Z= 0.243 Angle : 0.605 11.296 17829 Z= 0.318 Chirality : 0.045 0.224 2037 Planarity : 0.005 0.070 2226 Dihedral : 17.474 179.859 1939 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.44 % Allowed : 15.44 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.21), residues: 1589 helix: 2.53 (0.19), residues: 693 sheet: -0.66 (0.36), residues: 217 loop : -1.82 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 184 HIS 0.008 0.001 HIS C 320 PHE 0.012 0.001 PHE B 167 TYR 0.017 0.002 TYR D 174 ARG 0.017 0.000 ARG A 271 ********************** 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 248 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.6471 (mpt) cc_final: 0.5253 (mtp) REVERT: A 222 SER cc_start: 0.9037 (m) cc_final: 0.8827 (p) REVERT: B 263 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8437 (mptm) REVERT: B 281 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7128 (t80) REVERT: C 172 MET cc_start: 0.8417 (tpt) cc_final: 0.8137 (mmm) REVERT: C 320 HIS cc_start: 0.7555 (OUTLIER) cc_final: 0.5698 (p90) REVERT: D 140 MET cc_start: 0.6818 (mpm) cc_final: 0.5725 (ptt) REVERT: D 164 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8688 (mm) REVERT: E 164 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8815 (mm) REVERT: E 245 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.6212 (t80) REVERT: E 250 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8419 (mmtm) REVERT: E 281 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7197 (t80) REVERT: F 118 MET cc_start: 0.3995 (OUTLIER) cc_final: 0.2966 (ptp) REVERT: G 140 MET cc_start: 0.5296 (pmm) cc_final: 0.3863 (ptt) outliers start: 20 outliers final: 5 residues processed: 239 average time/residue: 1.6292 time to fit residues: 417.3930 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 : 2.065 ------------------------------------------------------------------------------- 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 D residue 164 LEU 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 130 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 125 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 320 HIS E 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.124963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.078626 restraints weight = 17884.948| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.39 r_work: 0.2800 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13160 Z= 0.165 Angle : 0.580 10.742 17829 Z= 0.298 Chirality : 0.043 0.232 2037 Planarity : 0.004 0.072 2226 Dihedral : 17.235 179.127 1939 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.30 % Allowed : 15.87 % Favored : 82.83 % 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: 0.54 (0.22), residues: 1589 helix: 2.61 (0.19), residues: 693 sheet: -0.66 (0.35), residues: 217 loop : -1.82 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 184 HIS 0.004 0.001 HIS E 137 PHE 0.014 0.001 PHE F 324 TYR 0.022 0.002 TYR C 174 ARG 0.017 0.000 ARG A 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6530.22 seconds wall clock time: 117 minutes 38.37 seconds (7058.37 seconds total)