Starting phenix.real_space_refine on Sun Jul 21 03:19:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4t_24177/07_2024/7n4t_24177.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4t_24177/07_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4t_24177/07_2024/7n4t_24177.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4t_24177/07_2024/7n4t_24177.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4t_24177/07_2024/7n4t_24177.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4t_24177/07_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 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 6.95, per 1000 atoms: 0.54 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: 4.81 Conformation dependent library (CDL) restraints added in 2.3 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: 1.29 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: 3.63 Time building geometry restraints manager: 5.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2031 1.31 - 1.44: 3583 1.44 - 1.56: 7409 1.56 - 1.69: 18 1.69 - 1.81: 119 Bond restraints: 13160 Sorted by residual: bond pdb=" CA GLU D 136 " pdb=" C GLU D 136 " ideal model delta sigma weight residual 1.523 1.592 -0.069 1.35e-02 5.49e+03 2.65e+01 bond pdb=" C GLY D 135 " pdb=" O GLY D 135 " ideal model delta sigma weight residual 1.234 1.186 0.048 1.19e-02 7.06e+03 1.61e+01 bond pdb=" CA TYR B 332 " pdb=" CB TYR B 332 " ideal model delta sigma weight residual 1.529 1.587 -0.058 1.58e-02 4.01e+03 1.36e+01 bond pdb=" C30 PEE F 401 " pdb=" O3 PEE F 401 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C30 PEE A 401 " pdb=" O3 PEE A 401 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 13155 not shown) Histogram of bond angle deviations from ideal: 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: 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 2.440 nonbonded pdb=" OG SER F 284 " pdb=" O PRO F 327 " model vdw 2.205 2.440 nonbonded pdb=" NH2 ARG E 244 " pdb=" OE2 GLU E 246 " model vdw 2.259 2.520 nonbonded pdb=" O LEU C 133 " pdb=" OG SER D 141 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR B 208 " pdb=" OD1 ASP B 210 " model vdw 2.277 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 35.250 Find NCS groups from input model: 0.890 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:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.950 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 290 time to evaluate : 1.465 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: 1.4784 time to fit residues: 462.9379 Evaluate side-chains 243 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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: 0.8980 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS B 329 GLN C 218 ASN E 137 HIS E 318 GLN F 234 ASN G 318 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1499 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= 0.222 Angle : 0.571 7.110 17829 Z= 0.306 Chirality : 0.045 0.181 2037 Planarity : 0.005 0.067 2226 Dihedral : 21.047 179.951 1939 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.09 % Allowed : 9.31 % Favored : 88.60 % 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: 2.32 (0.19), residues: 686 sheet: -1.05 (0.33), residues: 259 loop : -1.52 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 184 HIS 0.003 0.000 HIS G 137 PHE 0.022 0.002 PHE G 324 TYR 0.024 0.002 TYR E 174 ARG 0.006 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 283 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 254 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: A 140 MET cc_start: 0.7401 (mpp) cc_final: 0.6848 (pmm) REVERT: B 263 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8404 (mptm) REVERT: C 118 MET cc_start: 0.6596 (ttt) cc_final: 0.5593 (ptt) REVERT: E 250 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8480 (mmtm) REVERT: F 118 MET cc_start: 0.4604 (OUTLIER) cc_final: 0.3820 (ptp) REVERT: F 205 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8909 (ttmt) REVERT: F 263 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8128 (mptm) REVERT: G 247 ASP cc_start: 0.8449 (p0) cc_final: 0.8129 (p0) REVERT: G 263 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8518 (mptm) outliers start: 29 outliers final: 3 residues processed: 259 average time/residue: 1.4389 time to fit residues: 400.4299 Evaluate side-chains 249 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 240 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain G residue 263 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 95 optimal weight: 0.0010 chunk 38 optimal weight: 0.5980 chunk 140 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- 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: 0.8410 moved from start: 0.1745 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= 0.181 Angle : 0.520 7.566 17829 Z= 0.281 Chirality : 0.043 0.156 2037 Planarity : 0.004 0.064 2226 Dihedral : 19.960 171.443 1939 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.09 % Allowed : 10.53 % Favored : 87.37 % 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: 0.45 (0.21), residues: 1589 helix: 2.43 (0.19), residues: 686 sheet: -1.10 (0.33), residues: 259 loop : -1.51 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 184 HIS 0.013 0.001 HIS E 137 PHE 0.012 0.001 PHE C 281 TYR 0.024 0.002 TYR F 245 ARG 0.011 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 276 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 247 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.7242 (mpp) cc_final: 0.6864 (pmm) REVERT: A 222 SER cc_start: 0.8914 (m) cc_final: 0.8639 (p) REVERT: B 263 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8374 (mptm) REVERT: B 264 ASN cc_start: 0.8818 (m-40) cc_final: 0.8579 (m-40) REVERT: C 320 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.6482 (p-80) REVERT: D 140 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6642 (mpp) REVERT: E 245 TYR cc_start: 0.7878 (OUTLIER) cc_final: 0.6526 (t80) REVERT: E 250 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8457 (mmtm) REVERT: F 118 MET cc_start: 0.4645 (OUTLIER) cc_final: 0.3632 (ptp) REVERT: G 247 ASP cc_start: 0.8403 (p0) cc_final: 0.8001 (p0) outliers start: 29 outliers final: 9 residues processed: 255 average time/residue: 1.4456 time to fit residues: 396.1006 Evaluate side-chains 254 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 239 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain D residue 140 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 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: 1.9990 chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 94 optimal weight: 0.0040 chunk 140 optimal weight: 0.5980 chunk 148 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 40 optimal weight: 0.3980 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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: 0.8383 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13160 Z= 0.140 Angle : 0.491 6.463 17829 Z= 0.265 Chirality : 0.042 0.145 2037 Planarity : 0.004 0.060 2226 Dihedral : 19.102 178.223 1939 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.16 % Allowed : 11.62 % Favored : 86.22 % 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: 2.54 (0.20), residues: 686 sheet: -1.08 (0.33), residues: 259 loop : -1.49 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 184 HIS 0.004 0.000 HIS B 137 PHE 0.012 0.001 PHE F 324 TYR 0.024 0.001 TYR E 174 ARG 0.008 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 280 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 250 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: A 140 MET cc_start: 0.7015 (mpp) cc_final: 0.6702 (pmm) REVERT: A 222 SER cc_start: 0.8913 (m) cc_final: 0.8632 (p) REVERT: B 263 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8369 (mptm) REVERT: B 264 ASN cc_start: 0.8738 (m-40) cc_final: 0.8518 (m-40) REVERT: C 320 HIS cc_start: 0.7358 (OUTLIER) cc_final: 0.6413 (p-80) REVERT: E 245 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.6452 (t80) REVERT: E 250 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8414 (mmtm) REVERT: F 118 MET cc_start: 0.4235 (OUTLIER) cc_final: 0.3235 (ptp) REVERT: F 263 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8111 (mptm) REVERT: G 247 ASP cc_start: 0.8365 (p0) cc_final: 0.7930 (p0) outliers start: 30 outliers final: 7 residues processed: 259 average time/residue: 1.4709 time to fit residues: 408.3843 Evaluate side-chains 253 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 240 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 232 MET Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain G residue 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: 3.9990 chunk 84 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 76 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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: 0.8468 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13160 Z= 0.305 Angle : 0.579 8.137 17829 Z= 0.316 Chirality : 0.046 0.176 2037 Planarity : 0.005 0.071 2226 Dihedral : 18.800 174.307 1939 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.02 % Allowed : 12.55 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (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: 0.53 (0.21), residues: 1589 helix: 2.48 (0.19), residues: 693 sheet: -0.68 (0.35), residues: 217 loop : -1.67 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 184 HIS 0.003 0.000 HIS C 320 PHE 0.017 0.002 PHE D 209 TYR 0.017 0.002 TYR A 174 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 262 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 234 time to evaluate : 1.435 Fit side-chains revert: symmetry clash REVERT: A 140 MET cc_start: 0.6947 (mpp) cc_final: 0.6614 (pmm) REVERT: B 264 ASN cc_start: 0.8877 (m-40) cc_final: 0.8623 (m-40) REVERT: B 281 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7199 (t80) REVERT: C 320 HIS cc_start: 0.7494 (OUTLIER) cc_final: 0.6485 (p-80) REVERT: E 212 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.6860 (mtm180) REVERT: E 245 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.6531 (t80) REVERT: E 250 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8482 (mmtm) REVERT: E 333 MET cc_start: 0.8358 (mpp) cc_final: 0.8149 (mmt) REVERT: F 118 MET cc_start: 0.3893 (OUTLIER) cc_final: 0.3054 (ptp) REVERT: G 247 ASP cc_start: 0.8530 (p0) cc_final: 0.8046 (p0) outliers start: 28 outliers final: 9 residues processed: 246 average time/residue: 1.5227 time to fit residues: 401.3723 Evaluate side-chains 244 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 229 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain 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 G residue 158 MET Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.0170 chunk 134 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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: 0.8414 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 : 0.002 0.034 13160 Z= 0.156 Angle : 0.512 10.819 17829 Z= 0.276 Chirality : 0.043 0.140 2037 Planarity : 0.004 0.062 2226 Dihedral : 18.224 176.025 1939 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.80 % Allowed : 13.56 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.59 (0.22), residues: 1589 helix: 2.60 (0.19), residues: 693 sheet: -0.68 (0.35), residues: 217 loop : -1.70 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 184 HIS 0.001 0.000 HIS A 320 PHE 0.011 0.001 PHE F 324 TYR 0.024 0.001 TYR E 174 ARG 0.014 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 267 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 242 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.6753 (mpp) cc_final: 0.6479 (pmm) REVERT: A 222 SER cc_start: 0.8976 (m) cc_final: 0.8728 (p) REVERT: B 245 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.6964 (t80) REVERT: B 264 ASN cc_start: 0.8777 (m-40) cc_final: 0.8548 (m-40) REVERT: C 320 HIS cc_start: 0.7468 (OUTLIER) cc_final: 0.6369 (p-80) REVERT: D 222 SER cc_start: 0.8773 (m) cc_final: 0.8533 (p) REVERT: E 245 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.6487 (t80) REVERT: E 250 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8415 (mmtm) REVERT: F 118 MET cc_start: 0.3986 (OUTLIER) cc_final: 0.3119 (ptp) REVERT: G 247 ASP cc_start: 0.8438 (p0) cc_final: 0.7954 (p0) REVERT: G 263 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8532 (mptm) outliers start: 25 outliers final: 9 residues processed: 255 average time/residue: 1.4877 time to fit residues: 407.3380 Evaluate side-chains 252 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 237 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 263 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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: 0.8483 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13160 Z= 0.339 Angle : 0.596 9.458 17829 Z= 0.325 Chirality : 0.047 0.183 2037 Planarity : 0.005 0.073 2226 Dihedral : 18.058 178.130 1939 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.09 % Allowed : 14.43 % Favored : 83.48 % 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: 0.48 (0.21), residues: 1589 helix: 2.47 (0.19), residues: 693 sheet: -0.71 (0.35), residues: 217 loop : -1.72 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 184 HIS 0.003 0.000 HIS C 320 PHE 0.018 0.002 PHE D 209 TYR 0.024 0.002 TYR G 245 ARG 0.016 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 255 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 226 time to evaluate : 1.314 Fit side-chains revert: symmetry clash REVERT: A 140 MET cc_start: 0.6736 (mpp) cc_final: 0.6436 (pmm) REVERT: B 263 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8413 (mptm) REVERT: B 264 ASN cc_start: 0.8887 (m-40) cc_final: 0.8636 (m-40) REVERT: B 281 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7036 (t80) REVERT: C 320 HIS cc_start: 0.7589 (OUTLIER) cc_final: 0.6513 (p-80) REVERT: E 212 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.6897 (mtm180) REVERT: E 245 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.6834 (t80) REVERT: E 250 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8477 (mmtm) REVERT: F 118 MET cc_start: 0.3929 (OUTLIER) cc_final: 0.3050 (ptp) REVERT: F 333 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7324 (mmm) REVERT: G 247 ASP cc_start: 0.8546 (p0) cc_final: 0.8130 (p0) REVERT: G 263 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8597 (mptm) REVERT: G 333 MET cc_start: 0.7320 (mmm) cc_final: 0.6904 (mmt) outliers start: 29 outliers final: 7 residues processed: 239 average time/residue: 1.5622 time to fit residues: 399.8709 Evaluate side-chains 240 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 224 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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 210 ASP Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 263 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 73 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 135 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13160 Z= 0.167 Angle : 0.536 10.602 17829 Z= 0.287 Chirality : 0.043 0.139 2037 Planarity : 0.004 0.064 2226 Dihedral : 17.738 179.819 1939 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.73 % Allowed : 15.22 % Favored : 83.04 % 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: 0.56 (0.22), residues: 1589 helix: 2.61 (0.19), residues: 693 sheet: -0.71 (0.35), residues: 217 loop : -1.75 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 184 HIS 0.002 0.000 HIS A 320 PHE 0.012 0.001 PHE F 324 TYR 0.022 0.001 TYR G 245 ARG 0.015 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 260 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 236 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.6697 (mpp) cc_final: 0.6381 (pmm) REVERT: A 222 SER cc_start: 0.9021 (m) cc_final: 0.8777 (p) REVERT: B 193 GLU cc_start: 0.8574 (tp30) cc_final: 0.7472 (tm-30) REVERT: B 245 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.6934 (t80) REVERT: B 263 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8440 (mptm) REVERT: B 264 ASN cc_start: 0.8790 (m-40) cc_final: 0.8526 (m-40) REVERT: B 281 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.6940 (t80) REVERT: C 320 HIS cc_start: 0.7520 (OUTLIER) cc_final: 0.6339 (p-80) REVERT: D 177 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7765 (mtp85) REVERT: E 245 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.6518 (t80) REVERT: E 250 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8420 (mmtm) REVERT: F 118 MET cc_start: 0.3845 (OUTLIER) cc_final: 0.3015 (ptp) REVERT: G 244 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7840 (mtm180) REVERT: G 247 ASP cc_start: 0.8379 (p0) cc_final: 0.8000 (p0) REVERT: G 263 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8544 (mptm) outliers start: 24 outliers final: 8 residues processed: 248 average time/residue: 1.4915 time to fit residues: 396.3294 Evaluate side-chains 248 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 230 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 244 ARG Chi-restraints excluded: chain G residue 263 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.2964 > 50: distance: 50 - 73: 10.689 distance: 54 - 77: 21.644 distance: 64 - 85: 18.499 distance: 69 - 73: 11.142 distance: 70 - 93: 22.502 distance: 73 - 74: 3.936 distance: 74 - 75: 21.177 distance: 75 - 76: 17.057 distance: 75 - 77: 34.927 distance: 76 - 101: 14.950 distance: 77 - 78: 8.266 distance: 78 - 79: 9.922 distance: 78 - 81: 9.131 distance: 79 - 80: 28.801 distance: 79 - 85: 19.343 distance: 80 - 113: 14.852 distance: 81 - 82: 23.878 distance: 81 - 83: 16.602 distance: 82 - 84: 32.132 distance: 85 - 86: 17.444 distance: 86 - 87: 10.235 distance: 86 - 89: 19.072 distance: 87 - 88: 26.716 distance: 87 - 93: 11.902 distance: 88 - 124: 7.696 distance: 89 - 90: 35.250 distance: 90 - 91: 12.739 distance: 91 - 92: 42.886 distance: 93 - 94: 23.926 distance: 94 - 95: 22.461 distance: 94 - 97: 19.368 distance: 95 - 96: 13.495 distance: 95 - 101: 27.708 distance: 97 - 98: 15.822 distance: 98 - 99: 35.780 distance: 98 - 100: 12.422 distance: 101 - 102: 7.675 distance: 102 - 103: 12.986 distance: 102 - 105: 16.947 distance: 103 - 104: 7.648 distance: 103 - 113: 18.335 distance: 105 - 106: 6.794 distance: 106 - 107: 11.421 distance: 106 - 108: 13.873 distance: 107 - 109: 28.438 distance: 108 - 110: 11.058 distance: 109 - 111: 12.041 distance: 110 - 111: 9.664 distance: 111 - 112: 16.949 distance: 113 - 114: 11.700 distance: 114 - 115: 10.964 distance: 114 - 117: 13.658 distance: 115 - 116: 8.451 distance: 115 - 124: 6.628 distance: 117 - 118: 9.527 distance: 118 - 119: 9.161 distance: 118 - 120: 9.407 distance: 119 - 121: 16.837 distance: 120 - 122: 11.196 distance: 121 - 123: 10.340 distance: 122 - 123: 12.593 distance: 124 - 125: 14.973 distance: 125 - 126: 9.167 distance: 125 - 128: 8.097 distance: 126 - 127: 14.660 distance: 126 - 132: 13.359 distance: 128 - 129: 8.404 distance: 129 - 130: 3.603 distance: 129 - 131: 9.363 distance: 132 - 133: 9.193 distance: 133 - 134: 36.837 distance: 133 - 136: 10.723 distance: 134 - 135: 45.242 distance: 134 - 143: 43.967 distance: 136 - 137: 11.387 distance: 137 - 138: 17.897 distance: 138 - 139: 5.419 distance: 139 - 140: 6.015 distance: 140 - 141: 7.149 distance: 140 - 142: 7.789 distance: 143 - 144: 27.454 distance: 143 - 149: 29.177 distance: 144 - 145: 11.576 distance: 144 - 147: 19.198 distance: 145 - 146: 33.724 distance: 145 - 150: 44.929 distance: 147 - 148: 14.221 distance: 148 - 149: 17.533 distance: 150 - 151: 13.167 distance: 151 - 152: 23.218 distance: 151 - 154: 13.121 distance: 152 - 153: 9.637 distance: 152 - 161: 7.693 distance: 154 - 155: 27.225 distance: 155 - 156: 10.923 distance: 155 - 157: 15.979 distance: 156 - 158: 18.539 distance: 157 - 159: 32.727 distance: 158 - 160: 21.368 distance: 159 - 160: 25.304