Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 18:18:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4t_24177/04_2023/7n4t_24177_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4t_24177/04_2023/7n4t_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4t_24177/04_2023/7n4t_24177.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4t_24177/04_2023/7n4t_24177.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4t_24177/04_2023/7n4t_24177_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4t_24177/04_2023/7n4t_24177_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Residue "A PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "B ASP 189": "OD1" <-> "OD2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C ASP 210": "OD1" <-> "OD2" Residue "C PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 301": "OE1" <-> "OE2" Residue "C ASP 334": "OD1" <-> "OD2" Residue "D PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 189": "OD1" <-> "OD2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D ASP 210": "OD1" <-> "OD2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D GLU 246": "OE1" <-> "OE2" Residue "D ASP 283": "OD1" <-> "OD2" Residue "D GLU 301": "OE1" <-> "OE2" Residue "D TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "E TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 256": "OE1" <-> "OE2" Residue "E ASP 283": "OD1" <-> "OD2" Residue "E ASP 308": "OD1" <-> "OD2" Residue "E ASP 334": "OD1" <-> "OD2" Residue "F PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 189": "OD1" <-> "OD2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F GLU 301": "OE1" <-> "OE2" Residue "G ASP 189": "OD1" <-> "OD2" Residue "G GLU 198": "OE1" <-> "OE2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "G ASP 334": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 6.50, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 5.26 Conformation dependent library (CDL) restraints added in 1.8 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... running ksdssp... Secondary structure from input PDB file: 45 helices and 14 sheets defined 44.9% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 112 through 133 Processing helix chain 'A' and resid 135 through 138 No H-bonds generated for 'chain 'A' and resid 135 through 138' Processing helix chain 'A' and resid 142 through 175 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 218 through 222 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 301 through 319 Processing helix chain 'B' and resid 112 through 138 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 142 through 175 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 218 through 222 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 248 through 263 removed outlier: 5.111A pdb=" N GLY B 252 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 253 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 319 Processing helix chain 'C' and resid 113 through 138 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 142 through 175 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 218 through 222 Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 248 through 264 removed outlier: 4.901A pdb=" N GLY C 252 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 319 Processing helix chain 'D' and resid 113 through 133 Processing helix chain 'D' and resid 142 through 175 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 218 through 222 Processing helix chain 'D' and resid 229 through 231 No H-bonds generated for 'chain 'D' and resid 229 through 231' Processing helix chain 'D' and resid 248 through 264 removed outlier: 4.914A pdb=" N GLY D 252 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 319 Processing helix chain 'E' and resid 112 through 133 Processing helix chain 'E' and resid 135 through 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 142 through 175 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 218 through 222 Processing helix chain 'E' and resid 229 through 231 No H-bonds generated for 'chain 'E' and resid 229 through 231' Processing helix chain 'E' and resid 248 through 264 removed outlier: 4.635A pdb=" N GLY E 252 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL E 253 " --> pdb=" O LYS E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 319 Processing helix chain 'F' and resid 112 through 138 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 142 through 159 Processing helix chain 'F' and resid 162 through 175 Processing helix chain 'F' and resid 218 through 222 Processing helix chain 'F' and resid 229 through 231 No H-bonds generated for 'chain 'F' and resid 229 through 231' Processing helix chain 'F' and resid 248 through 263 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 301 through 319 Processing helix chain 'G' and resid 112 through 138 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 142 through 175 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 218 through 222 Processing helix chain 'G' and resid 229 through 231 No H-bonds generated for 'chain 'G' and resid 229 through 231' Processing helix chain 'G' and resid 248 through 264 removed outlier: 4.989A pdb=" N GLY G 252 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL G 253 " --> pdb=" O LYS G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 319 Processing sheet with id= A, first strand: chain 'A' and resid 213 through 217 removed outlier: 5.721A pdb=" N THR A 207 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL A 196 " --> pdb=" O THR A 207 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 236 through 240 Processing sheet with id= C, first strand: chain 'B' and resid 213 through 217 removed outlier: 5.531A pdb=" N THR B 207 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL B 196 " --> pdb=" O THR B 207 " (cutoff:3.500A) Processing sheet with id= D, 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= E, first strand: chain 'C' and resid 213 through 217 removed outlier: 5.395A pdb=" N THR C 207 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N VAL C 196 " --> pdb=" O THR C 207 " (cutoff:3.500A) Processing sheet with id= F, 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= G, first strand: chain 'D' and resid 213 through 217 removed outlier: 5.332A pdb=" N THR D 207 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N VAL D 196 " --> pdb=" O THR D 207 " (cutoff:3.500A) Processing sheet with id= H, 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= I, first strand: chain 'E' and resid 213 through 217 removed outlier: 5.613A pdb=" N THR E 207 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N VAL E 196 " --> pdb=" O THR E 207 " (cutoff:3.500A) Processing sheet with id= J, 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= K, first strand: chain 'F' and resid 213 through 217 removed outlier: 5.507A pdb=" N THR F 207 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL F 196 " --> pdb=" O THR F 207 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 236 through 240 Processing sheet with id= M, first strand: chain 'G' and resid 213 through 217 removed outlier: 5.436A pdb=" N THR G 207 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL G 196 " --> pdb=" O THR G 207 " (cutoff:3.500A) Processing sheet with id= N, 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) 626 hydrogen bonds defined for protein. 1632 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: 3.73 Time building geometry restraints manager: 5.63 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: 94.86 - 102.69: 62 102.69 - 110.52: 3799 110.52 - 118.35: 6319 118.35 - 126.18: 7444 126.18 - 134.01: 205 Bond angle restraints: 17829 Sorted by residual: angle pdb=" N LEU E 331 " pdb=" CA LEU E 331 " pdb=" C LEU E 331 " ideal model delta sigma weight residual 111.28 123.78 -12.50 1.09e+00 8.42e-01 1.32e+02 angle pdb=" N LEU G 331 " pdb=" CA LEU G 331 " pdb=" C LEU G 331 " ideal model delta sigma weight residual 111.36 123.63 -12.27 1.09e+00 8.42e-01 1.27e+02 angle pdb=" N LEU C 331 " pdb=" CA LEU C 331 " pdb=" C LEU C 331 " ideal model delta sigma weight residual 112.38 121.21 -8.83 1.22e+00 6.72e-01 5.24e+01 angle pdb=" N GLY D 135 " pdb=" CA GLY D 135 " pdb=" C GLY D 135 " ideal model delta sigma weight residual 112.77 103.53 9.24 1.28e+00 6.10e-01 5.21e+01 angle pdb=" N SER G 328 " pdb=" CA SER G 328 " pdb=" C SER G 328 " ideal model delta sigma weight residual 110.42 121.28 -10.86 1.55e+00 4.16e-01 4.91e+01 ... (remaining 17824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.49: 7641 34.49 - 68.99: 91 68.99 - 103.48: 20 103.48 - 137.98: 6 137.98 - 172.47: 5 Dihedral angle restraints: 7763 sinusoidal: 3143 harmonic: 4620 Sorted by residual: dihedral pdb=" CA ASP D 323 " pdb=" C ASP D 323 " pdb=" N PHE D 324 " pdb=" CA PHE D 324 " ideal model delta harmonic sigma weight residual 180.00 152.51 27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" C LEU G 331 " pdb=" N LEU G 331 " pdb=" CA LEU G 331 " pdb=" CB LEU G 331 " ideal model delta harmonic sigma weight residual -122.60 -134.95 12.35 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" CA LEU B 243 " pdb=" C LEU B 243 " pdb=" N ARG B 244 " pdb=" CA ARG B 244 " ideal model delta harmonic sigma weight residual -180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 7760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1945 0.106 - 0.213: 81 0.213 - 0.319: 3 0.319 - 0.425: 7 0.425 - 0.531: 1 Chirality restraints: 2037 Sorted by residual: chirality pdb=" CA LEU G 331 " pdb=" N LEU G 331 " pdb=" C LEU G 331 " pdb=" CB LEU G 331 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.06e+00 chirality pdb=" CA ASN G 335 " pdb=" N ASN G 335 " pdb=" C ASN G 335 " pdb=" CB ASN G 335 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA ASP E 334 " pdb=" N ASP E 334 " pdb=" C ASP E 334 " pdb=" CB ASP E 334 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 2034 not shown) Planarity restraints: 2226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO G 327 " -0.017 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C PRO G 327 " 0.057 2.00e-02 2.50e+03 pdb=" O PRO G 327 " -0.021 2.00e-02 2.50e+03 pdb=" N SER G 328 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 331 " -0.016 2.00e-02 2.50e+03 3.05e-02 9.31e+00 pdb=" C LEU D 331 " 0.053 2.00e-02 2.50e+03 pdb=" O LEU D 331 " -0.019 2.00e-02 2.50e+03 pdb=" N TYR D 332 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 136 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.10e+00 pdb=" C GLU D 136 " 0.052 2.00e-02 2.50e+03 pdb=" O GLU D 136 " -0.020 2.00e-02 2.50e+03 pdb=" N HIS D 137 " -0.017 2.00e-02 2.50e+03 ... (remaining 2223 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1249 2.74 - 3.28: 13314 3.28 - 3.82: 21398 3.82 - 4.36: 26040 4.36 - 4.90: 44861 Nonbonded interactions: 106862 Sorted by model distance: nonbonded pdb=" O LEU A 133 " pdb=" OG SER B 141 " model vdw 2.198 2.440 nonbonded pdb=" OG SER F 284 " pdb=" O PRO F 327 " model vdw 2.205 2.440 nonbonded pdb=" O GLY C 135 " pdb=" N GLY C 139 " model vdw 2.222 2.520 nonbonded pdb=" O GLY E 135 " pdb=" N GLY E 139 " model vdw 2.237 2.520 nonbonded pdb=" NH2 ARG E 244 " pdb=" OE2 GLU E 246 " model vdw 2.259 2.520 ... (remaining 106857 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.060 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: 0.000 Extract box with map and model: 4.590 Check model and map are aligned: 0.210 Set scattering table: 0.100 Process input model: 33.540 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.500 ------------------------------------------------------------------------------- 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= 0.298 Angle : 0.896 16.852 17829 Z= 0.474 Chirality : 0.052 0.531 2037 Planarity : 0.004 0.061 2226 Dihedral : 14.859 172.474 4795 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 0.14 % 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 *********************** 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 fitting. rotamer outliers: 2 poor density : 290 time to evaluate : 1.442 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 292 average time/residue: 1.5072 time to fit residues: 472.3333 Evaluate side-chains 242 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.491 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0379 ------------------------------------------------------------------------------- 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: 2.9990 chunk 116 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 73 optimal weight: 0.4980 chunk 89 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS C 218 ASN 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: 0.8457 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 13160 Z= 0.314 Angle : 0.595 6.826 17829 Z= 0.327 Chirality : 0.046 0.177 2037 Planarity : 0.005 0.074 2226 Dihedral : 13.254 178.868 1869 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 1.88 % 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: 0.06 (0.21), residues: 1589 helix: 1.93 (0.20), residues: 679 sheet: -1.01 (0.33), residues: 259 loop : -1.61 (0.22), residues: 651 *********************** 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 269 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 243 time to evaluate : 1.371 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 3 residues processed: 247 average time/residue: 1.5154 time to fit residues: 401.6913 Evaluate side-chains 237 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 234 time to evaluate : 1.452 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.6688 time to fit residues: 3.5756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 140 optimal weight: 0.0050 chunk 151 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 13160 Z= 0.163 Angle : 0.512 7.035 17829 Z= 0.281 Chirality : 0.043 0.157 2037 Planarity : 0.004 0.064 2226 Dihedral : 12.118 178.872 1869 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 1.66 % 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: -0.04 (0.21), residues: 1589 helix: 1.76 (0.20), residues: 686 sheet: -1.22 (0.33), residues: 273 loop : -1.49 (0.23), residues: 630 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 253 time to evaluate : 1.619 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 6 residues processed: 259 average time/residue: 1.4849 time to fit residues: 413.1468 Evaluate side-chains 249 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 243 time to evaluate : 1.508 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 3 average time/residue: 0.5265 time to fit residues: 3.9610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 94 optimal weight: 0.0050 chunk 140 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 13160 Z= 0.166 Angle : 0.505 7.234 17829 Z= 0.277 Chirality : 0.043 0.154 2037 Planarity : 0.004 0.066 2226 Dihedral : 11.461 177.374 1869 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 1.66 % 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: -0.05 (0.22), residues: 1589 helix: 1.72 (0.20), residues: 686 sheet: -1.17 (0.33), residues: 273 loop : -1.49 (0.23), residues: 630 *********************** 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 268 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 245 time to evaluate : 1.368 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 8 residues processed: 255 average time/residue: 1.4773 time to fit residues: 405.8663 Evaluate side-chains 248 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 240 time to evaluate : 1.497 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.9841 time to fit residues: 5.3618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 127 optimal weight: 0.2980 chunk 102 optimal weight: 0.6980 chunk 0 optimal weight: 40.0000 chunk 76 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 320 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1942 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= 0.159 Angle : 0.508 7.961 17829 Z= 0.276 Chirality : 0.043 0.152 2037 Planarity : 0.004 0.063 2226 Dihedral : 11.079 176.977 1869 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 1.30 % 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: -0.05 (0.21), residues: 1589 helix: 1.71 (0.20), residues: 686 sheet: -0.76 (0.36), residues: 231 loop : -1.66 (0.22), residues: 672 *********************** 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 262 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 244 time to evaluate : 1.468 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 251 average time/residue: 1.5505 time to fit residues: 418.0916 Evaluate side-chains 245 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 238 time to evaluate : 1.366 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.1397 time to fit residues: 3.2048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.0050 chunk 134 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 87 optimal weight: 0.0870 chunk 36 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 overall best weight: 0.7374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2040 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= 0.167 Angle : 0.515 13.604 17829 Z= 0.278 Chirality : 0.043 0.151 2037 Planarity : 0.004 0.062 2226 Dihedral : 10.702 177.512 1869 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 1.66 % 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: -0.03 (0.22), residues: 1589 helix: 1.76 (0.20), residues: 686 sheet: -0.73 (0.36), residues: 231 loop : -1.70 (0.22), residues: 672 *********************** 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 264 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 241 time to evaluate : 1.557 Fit side-chains outliers start: 23 outliers final: 7 residues processed: 252 average time/residue: 1.4941 time to fit residues: 403.8569 Evaluate side-chains 246 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 239 time to evaluate : 1.357 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 2 average time/residue: 0.1986 time to fit residues: 2.4455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 320 HIS D 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.039 13160 Z= 0.367 Angle : 0.624 11.309 17829 Z= 0.341 Chirality : 0.048 0.199 2037 Planarity : 0.005 0.077 2226 Dihedral : 10.598 179.130 1869 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 1.52 % 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: -0.07 (0.21), residues: 1589 helix: 1.68 (0.20), residues: 686 sheet: -0.39 (0.36), residues: 217 loop : -1.79 (0.22), residues: 686 *********************** 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 250 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 229 time to evaluate : 1.443 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 6 residues processed: 236 average time/residue: 1.5575 time to fit residues: 393.8268 Evaluate side-chains 236 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 230 time to evaluate : 1.531 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.4283 time to fit residues: 3.5882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 116 optimal weight: 0.0570 chunk 135 optimal weight: 5.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 13160 Z= 0.167 Angle : 0.537 10.023 17829 Z= 0.289 Chirality : 0.043 0.155 2037 Planarity : 0.005 0.073 2226 Dihedral : 10.079 179.525 1869 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 1.23 % 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: -0.06 (0.21), residues: 1589 helix: 1.76 (0.20), residues: 686 sheet: -0.77 (0.36), residues: 231 loop : -1.75 (0.22), residues: 672 *********************** 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 266 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 249 time to evaluate : 1.518 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 256 average time/residue: 1.5262 time to fit residues: 419.2853 Evaluate side-chains 240 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 233 time to evaluate : 1.562 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1693 time to fit residues: 2.7337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 108 optimal weight: 0.0970 chunk 42 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 130 optimal weight: 0.0970 chunk 137 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 13160 Z= 0.142 Angle : 0.524 9.405 17829 Z= 0.281 Chirality : 0.043 0.153 2037 Planarity : 0.004 0.064 2226 Dihedral : 9.735 177.732 1869 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 0.72 % 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: -0.04 (0.21), residues: 1589 helix: 1.80 (0.20), residues: 686 sheet: -0.77 (0.36), residues: 231 loop : -1.75 (0.22), residues: 672 *********************** 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 251 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 241 time to evaluate : 1.505 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 246 average time/residue: 1.5596 time to fit residues: 411.5081 Evaluate side-chains 238 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 233 time to evaluate : 1.364 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.9261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.0060 chunk 89 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 chunk 101 optimal weight: 0.0040 chunk 153 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 122 optimal weight: 0.0170 chunk 12 optimal weight: 0.9990 chunk 94 optimal weight: 0.2980 chunk 74 optimal weight: 3.9990 chunk 97 optimal weight: 0.3980 overall best weight: 0.1446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 13160 Z= 0.124 Angle : 0.524 14.079 17829 Z= 0.273 Chirality : 0.042 0.263 2037 Planarity : 0.004 0.058 2226 Dihedral : 9.346 178.711 1869 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.72 % 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: 0.07 (0.22), residues: 1589 helix: 1.90 (0.21), residues: 686 sheet: -0.77 (0.36), residues: 231 loop : -1.69 (0.23), residues: 672 ********************** 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 280 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 270 time to evaluate : 1.526 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 274 average time/residue: 1.4403 time to fit residues: 424.9381 Evaluate side-chains 257 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 252 time to evaluate : 1.493 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.3048 time to fit residues: 2.4784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 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: E 318 GLN G 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.126481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.080394 restraints weight = 17994.168| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.35 r_work: 0.2832 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 13160 Z= 0.162 Angle : 0.562 13.042 17829 Z= 0.294 Chirality : 0.044 0.302 2037 Planarity : 0.004 0.071 2226 Dihedral : 9.275 176.675 1869 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 0.72 % 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: 0.12 (0.22), residues: 1589 helix: 1.90 (0.21), residues: 686 sheet: -0.34 (0.36), residues: 217 loop : -1.75 (0.22), residues: 686 =============================================================================== Job complete usr+sys time: 6313.99 seconds wall clock time: 111 minutes 42.33 seconds (6702.33 seconds total)