Starting phenix.real_space_refine on Thu Feb 15 17:18:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4t_24177/02_2024/7n4t_24177_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4t_24177/02_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_24177/02_2024/7n4t_24177.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4t_24177/02_2024/7n4t_24177.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4t_24177/02_2024/7n4t_24177_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4t_24177/02_2024/7n4t_24177_updated.pdb" } 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-5238/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: 6.86, per 1000 atoms: 0.53 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: 5.25 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... 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: 2.35 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: 3.69 Time building geometry restraints manager: 5.59 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: 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: 0.680 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: 0.020 Extract box with map and model: 4.250 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 37.460 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 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: 56.080 ------------------------------------------------------------------------------- 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 : 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 : 1.388 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: 1.4615 time to fit residues: 458.4701 Evaluate side-chains 243 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.495 ------------------------------------------------------------------------------- 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 B 329 GLN C 218 ASN E 318 GLN F 234 ASN G 318 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1435 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= 0.310 Angle : 0.600 7.534 17829 Z= 0.329 Chirality : 0.047 0.183 2037 Planarity : 0.005 0.073 2226 Dihedral : 21.160 179.672 1939 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.73 % Allowed : 9.74 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1589 helix: 1.90 (0.20), residues: 679 sheet: -0.99 (0.33), residues: 259 loop : -1.62 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 184 HIS 0.002 0.000 HIS G 137 PHE 0.020 0.002 PHE G 324 TYR 0.025 0.002 TYR E 174 ARG 0.007 0.001 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 268 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 244 time to evaluate : 1.564 Fit side-chains REVERT: A 140 MET cc_start: 0.7593 (mpp) cc_final: 0.7210 (pmm) REVERT: C 118 MET cc_start: 0.6610 (ttt) cc_final: 0.5595 (ptt) REVERT: C 333 MET cc_start: 0.6374 (mmm) cc_final: 0.5816 (mmm) REVERT: D 193 GLU cc_start: 0.8623 (tt0) cc_final: 0.8416 (tt0) REVERT: E 212 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.6664 (mtm180) REVERT: F 118 MET cc_start: 0.4636 (OUTLIER) cc_final: 0.3829 (ptp) REVERT: G 247 ASP cc_start: 0.8473 (p0) cc_final: 0.8087 (p0) REVERT: G 263 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8423 (mptm) outliers start: 24 outliers final: 3 residues processed: 248 average time/residue: 1.4948 time to fit residues: 397.8660 Evaluate side-chains 239 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 233 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain F residue 118 MET 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: 3.9990 chunk 43 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 140 optimal weight: 0.1980 chunk 151 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1618 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= 0.186 Angle : 0.523 6.571 17829 Z= 0.286 Chirality : 0.043 0.160 2037 Planarity : 0.005 0.066 2226 Dihedral : 20.034 172.594 1939 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.09 % Allowed : 10.82 % Favored : 87.09 % 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: 1.80 (0.20), residues: 679 sheet: -1.22 (0.33), residues: 273 loop : -1.58 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 184 HIS 0.001 0.000 HIS C 320 PHE 0.012 0.001 PHE G 324 TYR 0.030 0.002 TYR F 245 ARG 0.008 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 280 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 251 time to evaluate : 1.567 Fit side-chains revert: symmetry clash REVERT: A 140 MET cc_start: 0.7508 (mpp) cc_final: 0.7151 (pmm) REVERT: C 140 MET cc_start: 0.7160 (mpp) cc_final: 0.6936 (pmm) REVERT: C 320 HIS cc_start: 0.7435 (OUTLIER) cc_final: 0.6443 (p-80) REVERT: E 245 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.6493 (t80) REVERT: F 118 MET cc_start: 0.4445 (OUTLIER) cc_final: 0.3467 (ptt) REVERT: F 263 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.7989 (mptm) REVERT: G 247 ASP cc_start: 0.8491 (p0) cc_final: 0.8092 (p0) REVERT: G 263 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8379 (mptm) outliers start: 29 outliers final: 7 residues processed: 259 average time/residue: 1.4616 time to fit residues: 407.3303 Evaluate side-chains 251 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 239 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain B residue 196 VAL 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 247 ASP Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 263 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 94 optimal weight: 0.0570 chunk 140 optimal weight: 2.9990 chunk 148 optimal weight: 0.3980 chunk 73 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 40 optimal weight: 0.0070 overall best weight: 0.8518 ------------------------------------------------------------------------------- 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: 0.8423 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13160 Z= 0.183 Angle : 0.518 8.450 17829 Z= 0.281 Chirality : 0.043 0.157 2037 Planarity : 0.004 0.064 2226 Dihedral : 19.408 174.290 1939 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.02 % Allowed : 11.83 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1589 helix: 1.73 (0.20), residues: 686 sheet: -0.80 (0.36), residues: 231 loop : -1.70 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 184 HIS 0.002 0.000 HIS C 320 PHE 0.010 0.001 PHE C 281 TYR 0.025 0.001 TYR E 174 ARG 0.007 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 241 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.7497 (mpp) cc_final: 0.7153 (pmm) REVERT: B 281 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7019 (t80) REVERT: C 320 HIS cc_start: 0.7432 (OUTLIER) cc_final: 0.6446 (p-80) REVERT: E 245 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.6453 (t80) REVERT: E 250 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8399 (mmtm) REVERT: F 118 MET cc_start: 0.4254 (OUTLIER) cc_final: 0.3239 (ptt) REVERT: F 263 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.7933 (mptm) REVERT: G 247 ASP cc_start: 0.8506 (p0) cc_final: 0.8081 (p0) REVERT: G 263 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8386 (mptm) outliers start: 28 outliers final: 9 residues processed: 251 average time/residue: 1.6418 time to fit residues: 441.5020 Evaluate side-chains 254 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 238 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.0000 chunk 84 optimal weight: 3.9990 chunk 2 optimal weight: 40.0000 chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 76 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 overall best weight: 1.4788 ------------------------------------------------------------------------------- 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: 0.8462 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13160 Z= 0.271 Angle : 0.560 8.035 17829 Z= 0.308 Chirality : 0.045 0.164 2037 Planarity : 0.005 0.070 2226 Dihedral : 18.959 177.760 1939 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.31 % Allowed : 12.41 % Favored : 85.28 % 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: -0.10 (0.21), residues: 1589 helix: 1.70 (0.20), residues: 686 sheet: -0.78 (0.36), residues: 231 loop : -1.73 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 184 HIS 0.003 0.000 HIS C 320 PHE 0.015 0.001 PHE D 209 TYR 0.017 0.002 TYR A 174 ARG 0.010 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 270 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 238 time to evaluate : 1.559 Fit side-chains revert: symmetry clash REVERT: A 140 MET cc_start: 0.7505 (mpp) cc_final: 0.7150 (pmm) REVERT: B 281 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7140 (t80) REVERT: C 320 HIS cc_start: 0.7495 (OUTLIER) cc_final: 0.6463 (p-80) REVERT: E 212 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.6734 (mtm180) REVERT: E 245 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.6553 (t80) REVERT: E 250 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8382 (mmtm) REVERT: F 118 MET cc_start: 0.4143 (OUTLIER) cc_final: 0.3260 (ptp) REVERT: F 263 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.7947 (mptm) REVERT: G 247 ASP cc_start: 0.8562 (p0) cc_final: 0.8125 (p0) REVERT: G 263 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8405 (mptm) REVERT: G 333 MET cc_start: 0.7451 (mmm) cc_final: 0.7132 (mmm) outliers start: 32 outliers final: 10 residues processed: 249 average time/residue: 1.5690 time to fit residues: 418.6702 Evaluate side-chains 248 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 230 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 263 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.0040 chunk 134 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 123 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- 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: 0.8420 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13160 Z= 0.166 Angle : 0.509 7.290 17829 Z= 0.277 Chirality : 0.043 0.155 2037 Planarity : 0.004 0.063 2226 Dihedral : 18.302 175.167 1939 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.88 % Allowed : 14.21 % Favored : 83.91 % 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: 1.75 (0.20), residues: 686 sheet: -0.77 (0.36), residues: 231 loop : -1.73 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 184 HIS 0.001 0.000 HIS C 320 PHE 0.013 0.001 PHE F 324 TYR 0.026 0.001 TYR E 174 ARG 0.011 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 245 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.7462 (mpp) cc_final: 0.7054 (pmm) REVERT: B 245 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.6908 (t80) REVERT: B 281 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.7031 (t80) REVERT: C 320 HIS cc_start: 0.7417 (OUTLIER) cc_final: 0.6299 (p-80) REVERT: E 245 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.6164 (t80) REVERT: E 250 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8382 (mmtm) REVERT: E 281 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7218 (t80) REVERT: F 118 MET cc_start: 0.4118 (OUTLIER) cc_final: 0.3252 (ptt) REVERT: F 263 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8001 (mptm) REVERT: G 247 ASP cc_start: 0.8471 (p0) cc_final: 0.7995 (p0) REVERT: G 263 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8329 (mptm) outliers start: 26 outliers final: 7 residues processed: 256 average time/residue: 1.5148 time to fit residues: 415.3826 Evaluate side-chains 250 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 234 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 245 TYR 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 245 TYR Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 298 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: 0.6980 chunk 16 optimal weight: 0.0980 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.8447 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13160 Z= 0.222 Angle : 0.550 14.184 17829 Z= 0.296 Chirality : 0.044 0.160 2037 Planarity : 0.005 0.066 2226 Dihedral : 17.982 177.394 1939 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.09 % Allowed : 14.72 % Favored : 83.19 % 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: 1.75 (0.20), residues: 686 sheet: -0.73 (0.36), residues: 231 loop : -1.75 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 184 HIS 0.002 0.000 HIS C 320 PHE 0.012 0.001 PHE D 209 TYR 0.028 0.002 TYR G 245 ARG 0.010 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 266 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 237 time to evaluate : 1.657 Fit side-chains REVERT: A 140 MET cc_start: 0.7457 (mpp) cc_final: 0.7073 (pmm) REVERT: B 193 GLU cc_start: 0.8542 (tp30) cc_final: 0.7587 (tm-30) REVERT: B 281 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7124 (t80) REVERT: C 320 HIS cc_start: 0.7402 (OUTLIER) cc_final: 0.6312 (p-80) REVERT: E 212 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.6742 (mtm180) REVERT: E 245 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.6623 (t80) REVERT: E 250 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8407 (mmtm) REVERT: F 118 MET cc_start: 0.3841 (OUTLIER) cc_final: 0.3028 (ptt) REVERT: F 263 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.7952 (mptm) REVERT: G 247 ASP cc_start: 0.8455 (p0) cc_final: 0.8067 (p0) REVERT: G 263 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8352 (mptm) outliers start: 29 outliers final: 8 residues processed: 250 average time/residue: 1.5040 time to fit residues: 402.7413 Evaluate side-chains 250 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 234 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 205 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 263 LYS Chi-restraints excluded: chain F residue 298 VAL 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: 1.9990 chunk 88 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 29 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.8434 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13160 Z= 0.197 Angle : 0.550 11.523 17829 Z= 0.292 Chirality : 0.044 0.156 2037 Planarity : 0.005 0.067 2226 Dihedral : 17.786 179.043 1939 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.59 % Allowed : 16.02 % Favored : 82.40 % 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: 1.77 (0.20), residues: 686 sheet: -0.74 (0.36), residues: 231 loop : -1.76 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 184 HIS 0.002 0.000 HIS C 320 PHE 0.012 0.001 PHE F 324 TYR 0.024 0.001 TYR E 174 ARG 0.016 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 236 time to evaluate : 1.529 Fit side-chains revert: symmetry clash REVERT: A 140 MET cc_start: 0.7382 (mpp) cc_final: 0.7013 (pmm) REVERT: B 281 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7056 (t80) REVERT: C 320 HIS cc_start: 0.7394 (OUTLIER) cc_final: 0.6179 (p-80) REVERT: E 212 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.6475 (mtm180) REVERT: E 245 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.6196 (t80) REVERT: E 250 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8403 (mmtm) REVERT: E 281 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7027 (t80) REVERT: F 118 MET cc_start: 0.3850 (OUTLIER) cc_final: 0.3016 (ptt) REVERT: F 263 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8017 (mptm) REVERT: G 247 ASP cc_start: 0.8414 (p0) cc_final: 0.8021 (p0) REVERT: G 263 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8376 (mptm) outliers start: 22 outliers final: 8 residues processed: 248 average time/residue: 1.5840 time to fit residues: 423.0290 Evaluate side-chains 250 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 233 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 205 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 E residue 281 PHE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 263 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8428 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13160 Z= 0.181 Angle : 0.540 10.313 17829 Z= 0.287 Chirality : 0.043 0.156 2037 Planarity : 0.005 0.067 2226 Dihedral : 17.603 179.538 1939 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.59 % Allowed : 15.95 % Favored : 82.47 % 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: 1.80 (0.20), residues: 686 sheet: -0.74 (0.36), residues: 231 loop : -1.75 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 184 HIS 0.002 0.000 HIS C 320 PHE 0.013 0.001 PHE F 324 TYR 0.018 0.001 TYR G 245 ARG 0.016 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 242 time to evaluate : 1.541 Fit side-chains REVERT: A 140 MET cc_start: 0.7366 (mpp) cc_final: 0.6989 (pmm) REVERT: B 245 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.6945 (t80) REVERT: B 281 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7053 (t80) REVERT: C 320 HIS cc_start: 0.7347 (OUTLIER) cc_final: 0.6141 (p-80) REVERT: C 333 MET cc_start: 0.7087 (mmm) cc_final: 0.6829 (mmm) REVERT: E 245 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.6200 (t80) REVERT: E 250 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8376 (mmtm) REVERT: E 281 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.7189 (t80) REVERT: F 118 MET cc_start: 0.3891 (OUTLIER) cc_final: 0.2852 (tpp) REVERT: F 263 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8009 (mptm) REVERT: G 247 ASP cc_start: 0.8415 (p0) cc_final: 0.8018 (p0) REVERT: G 263 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8355 (mptm) REVERT: G 333 MET cc_start: 0.7344 (mmm) cc_final: 0.7129 (mmt) outliers start: 22 outliers final: 9 residues processed: 255 average time/residue: 1.5095 time to fit residues: 413.2361 Evaluate side-chains 251 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 233 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 245 TYR 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 245 TYR Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 263 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 97 optimal weight: 0.0980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.8429 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13160 Z= 0.193 Angle : 0.558 10.522 17829 Z= 0.295 Chirality : 0.044 0.157 2037 Planarity : 0.005 0.070 2226 Dihedral : 17.478 179.714 1939 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.73 % Allowed : 16.09 % Favored : 82.18 % 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: -0.02 (0.22), residues: 1589 helix: 1.81 (0.20), residues: 686 sheet: -0.74 (0.36), residues: 231 loop : -1.75 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 184 HIS 0.002 0.000 HIS E 137 PHE 0.013 0.001 PHE E 138 TYR 0.018 0.001 TYR G 245 ARG 0.017 0.000 ARG A 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 234 time to evaluate : 1.634 Fit side-chains REVERT: A 140 MET cc_start: 0.7375 (mpp) cc_final: 0.7036 (pmm) REVERT: B 245 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.6944 (t80) REVERT: B 281 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7028 (t80) REVERT: C 140 MET cc_start: 0.6935 (mpp) cc_final: 0.6067 (mpp) REVERT: C 245 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.6864 (t80) REVERT: C 320 HIS cc_start: 0.7326 (OUTLIER) cc_final: 0.6220 (p-80) REVERT: D 164 LEU cc_start: 0.8874 (mm) cc_final: 0.8588 (mm) REVERT: E 245 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.6186 (t80) REVERT: E 250 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8388 (mmtm) REVERT: E 281 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7180 (t80) REVERT: F 118 MET cc_start: 0.3918 (OUTLIER) cc_final: 0.2821 (tpp) REVERT: F 263 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8029 (mptm) REVERT: G 247 ASP cc_start: 0.8429 (p0) cc_final: 0.8031 (p0) REVERT: G 263 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8348 (mptm) outliers start: 24 outliers final: 9 residues processed: 246 average time/residue: 1.5006 time to fit residues: 395.6171 Evaluate side-chains 251 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 232 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain 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 F residue 298 VAL Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 263 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 125 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.126780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.079497 restraints weight = 17872.224| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.41 r_work: 0.2816 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13160 Z= 0.147 Angle : 0.534 12.311 17829 Z= 0.282 Chirality : 0.043 0.185 2037 Planarity : 0.004 0.072 2226 Dihedral : 17.173 178.879 1939 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.44 % Allowed : 16.74 % Favored : 81.82 % 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: 0.00 (0.22), residues: 1589 helix: 1.86 (0.20), residues: 686 sheet: -0.76 (0.36), residues: 231 loop : -1.77 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 184 HIS 0.001 0.000 HIS C 320 PHE 0.016 0.001 PHE F 324 TYR 0.018 0.001 TYR G 245 ARG 0.017 0.000 ARG A 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6392.54 seconds wall clock time: 113 minutes 33.19 seconds (6813.19 seconds total)