Starting phenix.real_space_refine on Sat Apr 6 03:38:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8j_36071/04_2024/8j8j_36071_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8j_36071/04_2024/8j8j_36071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8j_36071/04_2024/8j8j_36071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8j_36071/04_2024/8j8j_36071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8j_36071/04_2024/8j8j_36071_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8j_36071/04_2024/8j8j_36071_updated.pdb" } resolution = 2.76 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= 0.002 sd= 0.101 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 3 5.21 5 S 30 5.16 5 C 4515 2.51 5 N 1104 2.21 5 O 1209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 24": "NH1" <-> "NH2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 239": "OE1" <-> "OE2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A ARG 207": "NH1" <-> "NH2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ASP 47": "OD1" <-> "OD2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6873 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2217 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "A" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2217 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "B" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2217 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {' MG': 1, 'PGW': 1, 'PRP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {' MG': 1, 'PGW': 1, 'PRP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {' MG': 1, 'PGW': 1, 'PRP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.48, per 1000 atoms: 0.65 Number of scatterers: 6873 At special positions: 0 Unit cell: (107.52, 99.84, 73.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 12 15.00 Mg 3 11.99 O 1209 8.00 N 1104 7.00 C 4515 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: 3.03 Conformation dependent library (CDL) restraints added in 1.2 seconds 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1614 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 0 sheets defined 71.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'D' and resid 14 through 17 No H-bonds generated for 'chain 'D' and resid 14 through 17' Processing helix chain 'D' and resid 23 through 38 removed outlier: 4.018A pdb=" N VAL D 27 " --> pdb=" O ARG D 24 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS D 28 " --> pdb=" O GLN D 25 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D 30 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU D 31 " --> pdb=" O LYS D 28 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 32 " --> pdb=" O ASN D 29 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALA D 35 " --> pdb=" O VAL D 32 " (cutoff:3.500A) Proline residue: D 36 - end of helix Processing helix chain 'D' and resid 50 through 76 removed outlier: 3.888A pdb=" N SER D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET D 57 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 124 through 140 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 148 through 167 removed outlier: 3.637A pdb=" N VAL D 153 " --> pdb=" O GLU D 149 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR D 157 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA D 161 " --> pdb=" O TYR D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 201 removed outlier: 3.552A pdb=" N GLU D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG D 201 " --> pdb=" O HIS D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 215 through 241 removed outlier: 3.505A pdb=" N PHE D 238 " --> pdb=" O GLY D 234 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 250 No H-bonds generated for 'chain 'D' and resid 247 through 250' Processing helix chain 'D' and resid 252 through 267 removed outlier: 3.650A pdb=" N VAL D 264 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP D 265 " --> pdb=" O ARG D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 280 removed outlier: 3.946A pdb=" N LEU D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 301 Processing helix chain 'A' and resid 14 through 17 No H-bonds generated for 'chain 'A' and resid 14 through 17' Processing helix chain 'A' and resid 23 through 38 removed outlier: 4.018A pdb=" N VAL A 27 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 28 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 30 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 31 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 32 " --> pdb=" O ASN A 29 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA A 35 " --> pdb=" O VAL A 32 " (cutoff:3.500A) Proline residue: A 36 - end of helix Processing helix chain 'A' and resid 50 through 76 removed outlier: 3.889A pdb=" N SER A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 120 Processing helix chain 'A' and resid 124 through 140 Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 148 through 167 removed outlier: 3.637A pdb=" N VAL A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 157 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 161 " --> pdb=" O TYR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 201 removed outlier: 3.552A pdb=" N GLU A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG A 201 " --> pdb=" O HIS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 215 through 241 removed outlier: 3.504A pdb=" N PHE A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 250 No H-bonds generated for 'chain 'A' and resid 247 through 250' Processing helix chain 'A' and resid 252 through 267 removed outlier: 3.650A pdb=" N VAL A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 280 removed outlier: 3.807A pdb=" N LEU A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 301 Processing helix chain 'B' and resid 14 through 17 No H-bonds generated for 'chain 'B' and resid 14 through 17' Processing helix chain 'B' and resid 23 through 38 removed outlier: 4.017A pdb=" N VAL B 27 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 28 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 30 " --> pdb=" O VAL B 27 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU B 31 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 32 " --> pdb=" O ASN B 29 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ALA B 35 " --> pdb=" O VAL B 32 " (cutoff:3.500A) Proline residue: B 36 - end of helix Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.889A pdb=" N SER B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 120 Processing helix chain 'B' and resid 124 through 140 Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 148 through 167 removed outlier: 3.637A pdb=" N VAL B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 161 " --> pdb=" O TYR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 201 removed outlier: 3.552A pdb=" N GLU B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 201 " --> pdb=" O HIS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 215 through 241 removed outlier: 3.504A pdb=" N PHE B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 250 No H-bonds generated for 'chain 'B' and resid 247 through 250' Processing helix chain 'B' and resid 252 through 267 removed outlier: 3.650A pdb=" N VAL B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 280 removed outlier: 3.882A pdb=" N LEU B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 301 390 hydrogen bonds defined for protein. 1134 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: 3.14 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1020 1.27 - 1.40: 1782 1.40 - 1.54: 4011 1.54 - 1.67: 157 1.67 - 1.81: 53 Bond restraints: 7023 Sorted by residual: bond pdb=" C1 PRP D 401 " pdb=" O4 PRP D 401 " ideal model delta sigma weight residual 1.656 1.418 0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C1 PRP A 401 " pdb=" O4 PRP A 401 " ideal model delta sigma weight residual 1.656 1.419 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1 PRP B 401 " pdb=" O4 PRP B 401 " ideal model delta sigma weight residual 1.656 1.420 0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C1 PRP A 401 " pdb=" C2 PRP A 401 " ideal model delta sigma weight residual 1.327 1.509 -0.182 2.00e-02 2.50e+03 8.27e+01 bond pdb=" C1 PRP B 401 " pdb=" C2 PRP B 401 " ideal model delta sigma weight residual 1.327 1.508 -0.181 2.00e-02 2.50e+03 8.23e+01 ... (remaining 7018 not shown) Histogram of bond angle deviations from ideal: 97.48 - 104.79: 129 104.79 - 112.11: 3559 112.11 - 119.42: 2312 119.42 - 126.74: 3440 126.74 - 134.06: 127 Bond angle restraints: 9567 Sorted by residual: angle pdb=" N ILE D 206 " pdb=" CA ILE D 206 " pdb=" C ILE D 206 " ideal model delta sigma weight residual 112.12 98.48 13.64 8.40e-01 1.42e+00 2.64e+02 angle pdb=" N ILE A 206 " pdb=" CA ILE A 206 " pdb=" C ILE A 206 " ideal model delta sigma weight residual 112.12 100.15 11.97 8.40e-01 1.42e+00 2.03e+02 angle pdb=" N ILE B 206 " pdb=" CA ILE B 206 " pdb=" C ILE B 206 " ideal model delta sigma weight residual 112.12 100.25 11.87 8.40e-01 1.42e+00 2.00e+02 angle pdb=" N ARG D 207 " pdb=" CA ARG D 207 " pdb=" C ARG D 207 " ideal model delta sigma weight residual 111.30 121.24 -9.94 1.36e+00 5.41e-01 5.34e+01 angle pdb=" N ARG D 207 " pdb=" CA ARG D 207 " pdb=" CB ARG D 207 " ideal model delta sigma weight residual 111.62 102.91 8.71 1.43e+00 4.89e-01 3.71e+01 ... (remaining 9562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.58: 3971 31.58 - 63.15: 160 63.15 - 94.73: 18 94.73 - 126.31: 6 126.31 - 157.89: 9 Dihedral angle restraints: 4164 sinusoidal: 1644 harmonic: 2520 Sorted by residual: dihedral pdb=" C LYS B 143 " pdb=" N LYS B 143 " pdb=" CA LYS B 143 " pdb=" CB LYS B 143 " ideal model delta harmonic sigma weight residual -122.60 -110.15 -12.45 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" C03 PGW B 403 " pdb=" C01 PGW B 403 " pdb=" C02 PGW B 403 " pdb=" O03 PGW B 403 " ideal model delta sinusoidal sigma weight residual -64.65 93.24 -157.89 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C03 PGW A 403 " pdb=" C01 PGW A 403 " pdb=" C02 PGW A 403 " pdb=" O03 PGW A 403 " ideal model delta sinusoidal sigma weight residual -64.65 93.23 -157.88 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 4161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1084 0.111 - 0.223: 33 0.223 - 0.334: 2 0.334 - 0.446: 6 0.446 - 0.557: 3 Chirality restraints: 1128 Sorted by residual: chirality pdb=" C02 PGW B 403 " pdb=" C01 PGW B 403 " pdb=" C03 PGW B 403 " pdb=" O01 PGW B 403 " both_signs ideal model delta sigma weight residual False 2.36 2.91 -0.56 2.00e-01 2.50e+01 7.76e+00 chirality pdb=" C02 PGW D 403 " pdb=" C01 PGW D 403 " pdb=" C03 PGW D 403 " pdb=" O01 PGW D 403 " both_signs ideal model delta sigma weight residual False 2.36 2.91 -0.56 2.00e-01 2.50e+01 7.72e+00 chirality pdb=" C02 PGW A 403 " pdb=" C01 PGW A 403 " pdb=" C03 PGW A 403 " pdb=" O01 PGW A 403 " both_signs ideal model delta sigma weight residual False 2.36 2.91 -0.55 2.00e-01 2.50e+01 7.69e+00 ... (remaining 1125 not shown) Planarity restraints: 1143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 169 " 0.013 2.00e-02 2.50e+03 2.73e-02 7.47e+00 pdb=" C LYS B 169 " -0.047 2.00e-02 2.50e+03 pdb=" O LYS B 169 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE B 170 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 169 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" C LYS A 169 " 0.046 2.00e-02 2.50e+03 pdb=" O LYS A 169 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE A 170 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 168 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.48e+00 pdb=" C THR D 168 " -0.044 2.00e-02 2.50e+03 pdb=" O THR D 168 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS D 169 " 0.015 2.00e-02 2.50e+03 ... (remaining 1140 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 10 2.35 - 2.99: 3419 2.99 - 3.63: 9521 3.63 - 4.26: 14991 4.26 - 4.90: 25556 Nonbonded interactions: 53497 Sorted by model distance: nonbonded pdb=" O3B PRP A 401 " pdb="MG MG A 402 " model vdw 1.717 2.170 nonbonded pdb=" O3B PRP B 401 " pdb="MG MG B 402 " model vdw 1.821 2.170 nonbonded pdb=" O3B PRP D 401 " pdb="MG MG D 402 " model vdw 1.836 2.170 nonbonded pdb=" O1A PRP A 401 " pdb="MG MG A 402 " model vdw 1.989 2.170 nonbonded pdb=" O1A PRP D 401 " pdb="MG MG D 402 " model vdw 2.000 2.170 ... (remaining 53492 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 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 6.460 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.160 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:22.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 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 : 0.011 0.238 7023 Z= 0.708 Angle : 1.193 13.645 9567 Z= 0.641 Chirality : 0.061 0.557 1128 Planarity : 0.005 0.034 1143 Dihedral : 19.317 157.885 2550 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Cbeta Deviations : 0.12 % 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: -2.54 (0.24), residues: 864 helix: -1.07 (0.18), residues: 663 sheet: None (None), residues: 0 loop : -3.37 (0.29), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 222 HIS 0.005 0.002 HIS D 197 PHE 0.014 0.002 PHE D 182 TYR 0.016 0.002 TYR A 217 ARG 0.005 0.000 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.740 Fit side-chains REVERT: D 212 SER cc_start: 0.8357 (m) cc_final: 0.8044 (p) REVERT: B 187 MET cc_start: 0.8118 (mmt) cc_final: 0.7898 (mmt) REVERT: B 270 LEU cc_start: 0.7196 (mt) cc_final: 0.6994 (mt) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 1.1292 time to fit residues: 112.8660 Evaluate side-chains 75 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 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 73 ASN B 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7023 Z= 0.168 Angle : 0.574 8.273 9567 Z= 0.288 Chirality : 0.039 0.188 1128 Planarity : 0.003 0.027 1143 Dihedral : 18.108 149.058 1176 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.38 % Allowed : 13.69 % Favored : 83.93 % 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: -0.58 (0.28), residues: 864 helix: 0.23 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -2.27 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 222 HIS 0.003 0.001 HIS D 197 PHE 0.011 0.002 PHE D 182 TYR 0.020 0.001 TYR D 213 ARG 0.002 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.773 Fit side-chains REVERT: D 45 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6219 (ttt90) REVERT: D 212 SER cc_start: 0.8216 (m) cc_final: 0.7926 (p) REVERT: A 142 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8283 (mp) REVERT: B 187 MET cc_start: 0.7969 (mmt) cc_final: 0.7726 (mmt) outliers start: 16 outliers final: 6 residues processed: 81 average time/residue: 1.0779 time to fit residues: 92.8676 Evaluate side-chains 78 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 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 73 ASN A 73 ASN B 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7023 Z= 0.165 Angle : 0.542 8.005 9567 Z= 0.275 Chirality : 0.038 0.185 1128 Planarity : 0.003 0.028 1143 Dihedral : 16.835 150.905 1176 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.12 % Allowed : 14.73 % Favored : 82.14 % 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: 0.33 (0.29), residues: 864 helix: 0.83 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.73 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 222 HIS 0.003 0.001 HIS D 197 PHE 0.012 0.002 PHE D 182 TYR 0.020 0.001 TYR D 213 ARG 0.001 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 0.791 Fit side-chains REVERT: D 45 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6201 (ttt90) REVERT: D 62 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.7452 (t80) REVERT: A 45 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6825 (ttt90) REVERT: A 62 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.8142 (t80) REVERT: A 142 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8138 (mp) REVERT: B 187 MET cc_start: 0.7971 (mmt) cc_final: 0.7748 (mmt) outliers start: 21 outliers final: 6 residues processed: 86 average time/residue: 1.0843 time to fit residues: 99.0865 Evaluate side-chains 83 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.5980 chunk 59 optimal weight: 0.0370 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 84 optimal weight: 0.0980 chunk 75 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 197 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7023 Z= 0.127 Angle : 0.501 7.272 9567 Z= 0.253 Chirality : 0.037 0.174 1128 Planarity : 0.003 0.026 1143 Dihedral : 15.926 150.810 1176 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.12 % Allowed : 15.92 % Favored : 80.95 % 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: 0.91 (0.30), residues: 864 helix: 1.24 (0.21), residues: 666 sheet: None (None), residues: 0 loop : -1.49 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 222 HIS 0.003 0.001 HIS A 197 PHE 0.008 0.001 PHE D 255 TYR 0.013 0.001 TYR D 213 ARG 0.001 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 0.766 Fit side-chains REVERT: D 45 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6204 (ttt90) REVERT: D 62 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.7352 (t80) REVERT: A 45 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6675 (ttt90) REVERT: A 62 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8216 (t80) REVERT: A 142 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8127 (mp) REVERT: B 56 SER cc_start: 0.8206 (OUTLIER) cc_final: 0.7969 (p) REVERT: B 187 MET cc_start: 0.7927 (mmt) cc_final: 0.7693 (mmt) outliers start: 21 outliers final: 4 residues processed: 82 average time/residue: 1.2005 time to fit residues: 104.2255 Evaluate side-chains 83 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 62 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.8132 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7023 Z= 0.223 Angle : 0.589 9.556 9567 Z= 0.296 Chirality : 0.040 0.205 1128 Planarity : 0.003 0.029 1143 Dihedral : 16.166 151.203 1176 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.12 % Allowed : 15.62 % Favored : 81.25 % 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: 0.69 (0.29), residues: 864 helix: 1.06 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -1.45 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 222 HIS 0.002 0.001 HIS B 197 PHE 0.016 0.002 PHE D 182 TYR 0.018 0.002 TYR D 213 ARG 0.002 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 70 time to evaluate : 0.705 Fit side-chains REVERT: D 45 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6309 (ttt90) REVERT: D 62 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.7372 (t80) REVERT: A 45 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6815 (ttt90) REVERT: A 62 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8170 (t80) REVERT: A 142 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8146 (mp) REVERT: B 187 MET cc_start: 0.8013 (mmt) cc_final: 0.7749 (mmt) outliers start: 21 outliers final: 11 residues processed: 85 average time/residue: 1.1162 time to fit residues: 100.7996 Evaluate side-chains 85 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.8158 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7023 Z= 0.285 Angle : 0.642 10.676 9567 Z= 0.322 Chirality : 0.043 0.222 1128 Planarity : 0.004 0.030 1143 Dihedral : 16.423 150.201 1176 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.42 % Allowed : 15.33 % Favored : 81.25 % 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 (0.29), residues: 864 helix: 0.83 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.34 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 222 HIS 0.003 0.001 HIS B 197 PHE 0.018 0.002 PHE D 182 TYR 0.018 0.002 TYR D 213 ARG 0.002 0.000 ARG D 240 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 72 time to evaluate : 0.743 Fit side-chains REVERT: D 45 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6308 (ttt90) REVERT: D 62 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.7388 (t80) REVERT: A 45 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6846 (ttt90) REVERT: A 62 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8199 (t80) REVERT: A 142 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8149 (mp) REVERT: B 187 MET cc_start: 0.8070 (mmt) cc_final: 0.7850 (mmt) outliers start: 23 outliers final: 10 residues processed: 88 average time/residue: 1.0974 time to fit residues: 102.4237 Evaluate side-chains 85 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 174 LYS Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8112 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7023 Z= 0.185 Angle : 0.559 8.302 9567 Z= 0.282 Chirality : 0.039 0.195 1128 Planarity : 0.003 0.029 1143 Dihedral : 15.924 147.631 1176 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.83 % Allowed : 16.96 % Favored : 80.21 % 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: 0.85 (0.29), residues: 864 helix: 1.12 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -1.16 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 222 HIS 0.002 0.001 HIS B 197 PHE 0.013 0.002 PHE D 182 TYR 0.014 0.001 TYR D 213 ARG 0.001 0.000 ARG D 240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 70 time to evaluate : 0.747 Fit side-chains REVERT: D 45 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6300 (ttt90) REVERT: D 62 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.7409 (t80) REVERT: A 45 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6617 (ttt90) REVERT: A 62 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8250 (t80) REVERT: A 142 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8107 (mp) REVERT: B 187 MET cc_start: 0.7989 (mmt) cc_final: 0.7753 (mmt) outliers start: 19 outliers final: 10 residues processed: 83 average time/residue: 1.0919 time to fit residues: 96.3010 Evaluate side-chains 85 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7023 Z= 0.163 Angle : 0.544 8.109 9567 Z= 0.272 Chirality : 0.038 0.184 1128 Planarity : 0.003 0.028 1143 Dihedral : 15.528 145.550 1176 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.83 % Allowed : 17.41 % Favored : 79.76 % 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: 1.13 (0.29), residues: 864 helix: 1.31 (0.21), residues: 663 sheet: None (None), residues: 0 loop : -1.01 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 222 HIS 0.003 0.001 HIS A 197 PHE 0.011 0.002 PHE A 182 TYR 0.012 0.001 TYR D 213 ARG 0.001 0.000 ARG D 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 0.718 Fit side-chains REVERT: D 45 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6283 (ttt90) REVERT: D 62 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.7406 (t80) REVERT: D 212 SER cc_start: 0.8221 (m) cc_final: 0.7972 (p) REVERT: A 45 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6677 (ttt90) REVERT: A 62 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8135 (t80) REVERT: A 142 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8106 (mp) REVERT: B 187 MET cc_start: 0.7974 (mmt) cc_final: 0.7757 (mmt) outliers start: 19 outliers final: 7 residues processed: 85 average time/residue: 1.1015 time to fit residues: 99.4321 Evaluate side-chains 81 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7023 Z= 0.182 Angle : 0.564 8.496 9567 Z= 0.282 Chirality : 0.039 0.191 1128 Planarity : 0.003 0.028 1143 Dihedral : 15.532 144.184 1176 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.79 % Allowed : 18.60 % Favored : 79.61 % 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: 1.10 (0.29), residues: 864 helix: 1.24 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.88 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 222 HIS 0.003 0.001 HIS A 197 PHE 0.013 0.002 PHE D 182 TYR 0.013 0.001 TYR D 213 ARG 0.001 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.670 Fit side-chains REVERT: D 45 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6496 (ttt90) REVERT: D 62 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.7382 (t80) REVERT: A 45 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6641 (ttt90) REVERT: A 62 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8130 (t80) REVERT: A 142 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8128 (mp) REVERT: B 187 MET cc_start: 0.7988 (mmt) cc_final: 0.7755 (mmt) outliers start: 12 outliers final: 7 residues processed: 77 average time/residue: 1.1533 time to fit residues: 94.1334 Evaluate side-chains 79 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 73 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8075 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7023 Z= 0.150 Angle : 0.536 8.616 9567 Z= 0.267 Chirality : 0.038 0.180 1128 Planarity : 0.003 0.027 1143 Dihedral : 15.215 141.270 1176 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.93 % Allowed : 18.60 % Favored : 79.46 % 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: 1.37 (0.29), residues: 864 helix: 1.43 (0.21), residues: 666 sheet: None (None), residues: 0 loop : -0.74 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 222 HIS 0.001 0.000 HIS D 197 PHE 0.010 0.002 PHE D 182 TYR 0.011 0.001 TYR D 213 ARG 0.001 0.000 ARG D 240 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.737 Fit side-chains REVERT: D 45 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6316 (ttt90) REVERT: D 62 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.7379 (t80) REVERT: A 45 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6650 (ttt90) REVERT: A 62 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8156 (t80) REVERT: A 142 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8115 (mp) REVERT: B 187 MET cc_start: 0.7958 (mmt) cc_final: 0.7736 (mmt) outliers start: 13 outliers final: 6 residues processed: 77 average time/residue: 1.2229 time to fit residues: 99.5602 Evaluate side-chains 79 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 12 optimal weight: 0.4980 chunk 60 optimal weight: 0.3980 chunk 3 optimal weight: 0.0970 chunk 49 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.162544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.102713 restraints weight = 6980.377| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.19 r_work: 0.2941 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7023 Z= 0.128 Angle : 0.521 9.624 9567 Z= 0.257 Chirality : 0.037 0.168 1128 Planarity : 0.003 0.027 1143 Dihedral : 14.632 137.832 1176 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.64 % Allowed : 19.05 % Favored : 79.32 % 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: 1.73 (0.30), residues: 864 helix: 1.68 (0.21), residues: 666 sheet: None (None), residues: 0 loop : -0.58 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 222 HIS 0.004 0.001 HIS A 197 PHE 0.009 0.001 PHE A 220 TYR 0.009 0.001 TYR D 213 ARG 0.001 0.000 ARG D 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2447.19 seconds wall clock time: 44 minutes 56.87 seconds (2696.87 seconds total)