Starting phenix.real_space_refine on Sat Aug 3 21:40:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7t_36941/08_2024/8k7t_36941.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7t_36941/08_2024/8k7t_36941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7t_36941/08_2024/8k7t_36941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7t_36941/08_2024/8k7t_36941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7t_36941/08_2024/8k7t_36941.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7t_36941/08_2024/8k7t_36941.cif" } resolution = 3.71 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= 0.001 sd= 0.124 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 5722 2.51 5 N 1451 2.21 5 O 1732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 156": "OE1" <-> "OE2" Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 138": "OD1" <-> "OD2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "E ASP 198": "OD1" <-> "OD2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 321": "OE1" <-> "OE2" Residue "E GLU 323": "OE1" <-> "OE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E GLU 378": "OE1" <-> "OE2" Residue "F GLU 102": "OE1" <-> "OE2" Residue "F ASP 109": "OD1" <-> "OD2" Residue "F TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "F ASP 144": "OD1" <-> "OD2" Residue "F GLU 169": "OE1" <-> "OE2" Residue "F GLU 175": "OE1" <-> "OE2" Residue "F GLU 200": "OE1" <-> "OE2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "F TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 276": "OD1" <-> "OD2" Residue "F ASP 288": "OD1" <-> "OD2" Residue "F GLU 311": "OE1" <-> "OE2" Residue "F TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 378": "OE1" <-> "OE2" Residue "F PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8948 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1743 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 208} Chain: "G" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "H" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 341 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "B" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1247 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "E" Number of atoms: 2511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2511 Classifications: {'peptide': 315} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 294} Chain: "F" Number of atoms: 2511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2511 Classifications: {'peptide': 315} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 294} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.10, per 1000 atoms: 0.57 Number of scatterers: 8948 At special positions: 0 Unit cell: (87.15, 102.09, 163.095, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1732 8.00 N 1451 7.00 C 5722 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS G 25 " - pdb=" SG CYS H 25 " distance=2.04 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 180 " distance=2.03 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 226 " - pdb=" SG CYS E 285 " distance=2.04 Simple disulfide: pdb=" SG CYS E 330 " - pdb=" SG CYS E 392 " distance=2.03 Simple disulfide: pdb=" SG CYS F 121 " - pdb=" SG CYS F 180 " distance=2.04 Simple disulfide: pdb=" SG CYS F 226 " - pdb=" SG CYS F 285 " distance=2.03 Simple disulfide: pdb=" SG CYS F 330 " - pdb=" SG CYS F 392 " distance=2.03 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 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 301 " - " ASN A 73 " " NAG A 302 " - " ASN A 167 " " NAG A 303 " - " ASN A 152 " " NAG C 1 " - " ASN A 66 " " NAG D 1 " - " ASN A 106 " " NAG E 501 " - " ASN E 238 " " NAG E 502 " - " ASN E 166 " " NAG F 501 " - " ASN F 166 " " NAG F 502 " - " ASN F 238 " " NAG I 1 " - " ASN E 261 " " NAG J 1 " - " ASN F 261 " Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 1.5 seconds 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 19 sheets defined 28.9% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.834A pdb=" N LEU A 55 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN A 56 " --> pdb=" O ASN A 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 56' Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.539A pdb=" N GLN A 204 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 236 Processing helix chain 'G' and resid 23 through 58 Processing helix chain 'H' and resid 21 through 62 removed outlier: 3.947A pdb=" N CYS H 25 " --> pdb=" O GLU H 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 75 removed outlier: 5.183A pdb=" N LYS B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LYS B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B 49 " --> pdb=" O PHE B 45 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLU B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 112 removed outlier: 3.680A pdb=" N ARG B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 154 removed outlier: 4.041A pdb=" N GLY B 121 " --> pdb=" O TYR B 117 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 199 Processing helix chain 'E' and resid 168 through 174 removed outlier: 3.588A pdb=" N SER E 174 " --> pdb=" O GLN E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 218 Processing helix chain 'E' and resid 273 through 280 removed outlier: 3.858A pdb=" N TRP E 277 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E 278 " --> pdb=" O ALA E 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 174 Processing helix chain 'F' and resid 212 through 218 Processing helix chain 'F' and resid 273 through 280 removed outlier: 3.942A pdb=" N TRP F 277 " --> pdb=" O VAL F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 386 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 33 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.839A pdb=" N ILE A 39 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 116 Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 121 removed outlier: 4.507A pdb=" N TYR A 177 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LYS A 141 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 142 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR A 153 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TYR A 144 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA6, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.682A pdb=" N GLY A 125 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N PHE A 127 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ARG A 162 " --> pdb=" O PHE A 127 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 100 through 105 removed outlier: 4.743A pdb=" N ALA E 159 " --> pdb=" O GLY E 125 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLU E 154 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N SER E 160 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL E 150 " --> pdb=" O CYS E 162 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS E 164 " --> pdb=" O GLN E 148 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN E 148 " --> pdb=" O LYS E 164 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AA9, first strand: chain 'E' and resid 208 through 209 removed outlier: 3.756A pdb=" N THR E 225 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP E 230 " --> pdb=" O THR E 264 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR E 264 " --> pdb=" O ASP E 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 238 through 243 Processing sheet with id=AB2, first strand: chain 'E' and resid 311 through 315 removed outlier: 4.257A pdb=" N THR E 329 " --> pdb=" O PHE E 315 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N PHE E 371 " --> pdb=" O ASN E 334 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 311 through 315 removed outlier: 4.257A pdb=" N THR E 329 " --> pdb=" O PHE E 315 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N PHE E 371 " --> pdb=" O ASN E 334 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 362 " --> pdb=" O PHE E 372 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 341 through 344 removed outlier: 3.820A pdb=" N LYS E 407 " --> pdb=" O CYS E 392 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 100 through 105 Processing sheet with id=AB6, first strand: chain 'F' and resid 134 through 136 Processing sheet with id=AB7, first strand: chain 'F' and resid 205 through 209 removed outlier: 3.656A pdb=" N ILE F 205 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP F 230 " --> pdb=" O THR F 264 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR F 264 " --> pdb=" O ASP F 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 238 through 243 Processing sheet with id=AB9, first strand: chain 'F' and resid 311 through 315 removed outlier: 4.287A pdb=" N THR F 329 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 349 through 350 439 hydrogen bonds defined for protein. 1197 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: 2.55 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1412 1.30 - 1.43: 2385 1.43 - 1.56: 5297 1.56 - 1.69: 2 1.69 - 1.82: 53 Bond restraints: 9149 Sorted by residual: bond pdb=" C PHE A 207 " pdb=" O PHE A 207 " ideal model delta sigma weight residual 1.238 1.173 0.065 1.28e-02 6.10e+03 2.59e+01 bond pdb=" C ILE A 206 " pdb=" O ILE A 206 " ideal model delta sigma weight residual 1.237 1.186 0.052 1.17e-02 7.31e+03 1.95e+01 bond pdb=" C ILE A 213 " pdb=" O ILE A 213 " ideal model delta sigma weight residual 1.237 1.188 0.049 1.13e-02 7.83e+03 1.88e+01 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C VAL A 211 " pdb=" O VAL A 211 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.17e-02 7.31e+03 1.68e+01 ... (remaining 9144 not shown) Histogram of bond angle deviations from ideal: 96.42 - 103.95: 121 103.95 - 111.47: 4387 111.47 - 119.00: 3240 119.00 - 126.53: 4529 126.53 - 134.05: 166 Bond angle restraints: 12443 Sorted by residual: angle pdb=" CB GLU B 171 " pdb=" CG GLU B 171 " pdb=" CD GLU B 171 " ideal model delta sigma weight residual 112.60 96.42 16.18 1.70e+00 3.46e-01 9.06e+01 angle pdb=" C ILE A 213 " pdb=" CA ILE A 213 " pdb=" CB ILE A 213 " ideal model delta sigma weight residual 111.97 102.70 9.27 1.28e+00 6.10e-01 5.24e+01 angle pdb=" N LEU A 205 " pdb=" CA LEU A 205 " pdb=" C LEU A 205 " ideal model delta sigma weight residual 113.18 105.05 8.13 1.21e+00 6.83e-01 4.52e+01 angle pdb=" N GLU B 171 " pdb=" CA GLU B 171 " pdb=" C GLU B 171 " ideal model delta sigma weight residual 111.03 103.75 7.28 1.11e+00 8.12e-01 4.30e+01 angle pdb=" C ARG A 179 " pdb=" CA ARG A 179 " pdb=" CB ARG A 179 " ideal model delta sigma weight residual 110.42 123.45 -13.03 1.99e+00 2.53e-01 4.29e+01 ... (remaining 12438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.44: 5298 24.44 - 48.89: 384 48.89 - 73.33: 51 73.33 - 97.78: 34 97.78 - 122.22: 22 Dihedral angle restraints: 5789 sinusoidal: 2598 harmonic: 3191 Sorted by residual: dihedral pdb=" CB CYS G 25 " pdb=" SG CYS G 25 " pdb=" SG CYS H 25 " pdb=" CB CYS H 25 " ideal model delta sinusoidal sigma weight residual -86.00 -175.19 89.19 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" N GLU B 171 " pdb=" C GLU B 171 " pdb=" CA GLU B 171 " pdb=" CB GLU B 171 " ideal model delta harmonic sigma weight residual 122.80 107.21 15.59 0 2.50e+00 1.60e-01 3.89e+01 dihedral pdb=" C GLU B 171 " pdb=" N GLU B 171 " pdb=" CA GLU B 171 " pdb=" CB GLU B 171 " ideal model delta harmonic sigma weight residual -122.60 -107.65 -14.95 0 2.50e+00 1.60e-01 3.58e+01 ... (remaining 5786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1417 0.098 - 0.196: 77 0.196 - 0.293: 10 0.293 - 0.391: 5 0.391 - 0.489: 1 Chirality restraints: 1510 Sorted by residual: chirality pdb=" CA GLU B 171 " pdb=" N GLU B 171 " pdb=" C GLU B 171 " pdb=" CB GLU B 171 " both_signs ideal model delta sigma weight residual False 2.51 3.00 -0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CA ILE A 213 " pdb=" N ILE A 213 " pdb=" C ILE A 213 " pdb=" CB ILE A 213 " both_signs ideal model delta sigma weight residual False 2.43 2.82 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" C1 NAG E 501 " pdb=" ND2 ASN E 238 " pdb=" C2 NAG E 501 " pdb=" O5 NAG E 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 1507 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 204 " 0.024 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C GLN A 204 " -0.084 2.00e-02 2.50e+03 pdb=" O GLN A 204 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU A 205 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 171 " 0.020 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" CD GLU B 171 " -0.073 2.00e-02 2.50e+03 pdb=" OE1 GLU B 171 " 0.027 2.00e-02 2.50e+03 pdb=" OE2 GLU B 171 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 200 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C GLU F 200 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU F 200 " 0.023 2.00e-02 2.50e+03 pdb=" N PRO F 201 " 0.021 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 104 2.60 - 3.18: 7586 3.18 - 3.75: 13419 3.75 - 4.33: 18061 4.33 - 4.90: 29961 Nonbonded interactions: 69131 Sorted by model distance: nonbonded pdb=" O LEU A 203 " pdb=" N ILE A 206 " model vdw 2.026 3.120 nonbonded pdb=" OE1 GLN E 118 " pdb=" NZ LYS E 164 " model vdw 2.198 3.120 nonbonded pdb=" O ASP A 168 " pdb=" OH TYR A 172 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR E 120 " pdb=" OE2 GLU F 102 " model vdw 2.278 3.040 nonbonded pdb=" O TYR B 193 " pdb=" NE2 GLN B 197 " model vdw 2.284 3.120 ... (remaining 69126 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 22 through 58) } ncs_group { reference = chain 'I' selection = chain 'J' } 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 group one per residue 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.420 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 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 : 0.005 0.085 9149 Z= 0.309 Angle : 0.853 16.180 12443 Z= 0.461 Chirality : 0.053 0.489 1510 Planarity : 0.005 0.070 1519 Dihedral : 18.711 122.219 3683 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.16 % Favored : 93.47 % Rotamer: Outliers : 0.61 % Allowed : 12.59 % Favored : 86.80 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 10.64 % 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: 0.17 (0.26), residues: 1072 helix: 2.02 (0.31), residues: 265 sheet: 0.26 (0.27), residues: 364 loop : -1.19 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 172 HIS 0.008 0.001 HIS E 105 PHE 0.013 0.001 PHE A 207 TYR 0.018 0.001 TYR F 313 ARG 0.008 0.001 ARG E 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 252 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 43 TYR cc_start: 0.8488 (t80) cc_final: 0.8124 (t80) REVERT: H 26 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.6471 (m-80) REVERT: H 28 LEU cc_start: 0.8222 (tt) cc_final: 0.7979 (tt) REVERT: B 123 LEU cc_start: 0.8378 (tp) cc_final: 0.7901 (tt) REVERT: E 135 TRP cc_start: 0.8321 (m100) cc_final: 0.7796 (m-10) outliers start: 6 outliers final: 2 residues processed: 257 average time/residue: 0.2040 time to fit residues: 72.4350 Evaluate side-chains 193 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 190 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain H residue 26 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN B 126 ASN ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 GLN ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9149 Z= 0.264 Angle : 0.717 10.456 12443 Z= 0.353 Chirality : 0.047 0.329 1510 Planarity : 0.004 0.055 1519 Dihedral : 14.247 110.799 1631 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.22 % Favored : 94.31 % Rotamer: Outliers : 3.05 % Allowed : 18.27 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1072 helix: 1.68 (0.30), residues: 260 sheet: 0.23 (0.27), residues: 378 loop : -1.18 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 42 HIS 0.003 0.001 HIS E 396 PHE 0.022 0.002 PHE E 335 TYR 0.022 0.002 TYR B 193 ARG 0.006 0.001 ARG G 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 196 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7689 (t) REVERT: G 43 TYR cc_start: 0.8468 (t80) cc_final: 0.8251 (t80) REVERT: H 26 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.6467 (m-80) REVERT: B 81 ASP cc_start: 0.8610 (p0) cc_final: 0.8211 (p0) REVERT: B 83 GLU cc_start: 0.7681 (pm20) cc_final: 0.7356 (pm20) REVERT: E 281 TYR cc_start: 0.7833 (m-10) cc_final: 0.7595 (m-10) outliers start: 30 outliers final: 16 residues processed: 214 average time/residue: 0.1953 time to fit residues: 57.8342 Evaluate side-chains 186 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 258 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 85 optimal weight: 0.3980 chunk 95 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 GLN ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9149 Z= 0.220 Angle : 0.675 8.090 12443 Z= 0.334 Chirality : 0.047 0.356 1510 Planarity : 0.004 0.056 1519 Dihedral : 12.301 108.845 1627 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.69 % Favored : 93.94 % Rotamer: Outliers : 4.06 % Allowed : 18.78 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -0.02 (0.26), residues: 1072 helix: 1.60 (0.30), residues: 261 sheet: 0.20 (0.27), residues: 383 loop : -1.20 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 42 HIS 0.005 0.001 HIS E 105 PHE 0.019 0.002 PHE B 148 TYR 0.019 0.001 TYR B 193 ARG 0.005 0.001 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 184 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.7917 (tp) cc_final: 0.7612 (tt) REVERT: A 226 GLU cc_start: 0.8064 (pt0) cc_final: 0.7798 (pp20) REVERT: H 26 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.6118 (m-10) REVERT: B 51 GLU cc_start: 0.7294 (mp0) cc_final: 0.6860 (mp0) REVERT: B 81 ASP cc_start: 0.8640 (p0) cc_final: 0.8409 (p0) REVERT: B 83 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7420 (pm20) REVERT: B 171 GLU cc_start: 0.7090 (tt0) cc_final: 0.6625 (tt0) REVERT: E 281 TYR cc_start: 0.7969 (m-10) cc_final: 0.7685 (m-10) REVERT: E 296 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7917 (pt) outliers start: 40 outliers final: 25 residues processed: 208 average time/residue: 0.2043 time to fit residues: 58.5156 Evaluate side-chains 201 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 241 TRP Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 330 CYS Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 392 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 85 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9149 Z= 0.207 Angle : 0.661 8.197 12443 Z= 0.329 Chirality : 0.046 0.360 1510 Planarity : 0.004 0.060 1519 Dihedral : 11.218 105.656 1627 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.78 % Favored : 93.94 % Rotamer: Outliers : 4.26 % Allowed : 20.00 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 1072 helix: 1.54 (0.31), residues: 261 sheet: 0.16 (0.27), residues: 376 loop : -1.19 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 42 HIS 0.004 0.001 HIS E 105 PHE 0.021 0.001 PHE B 148 TYR 0.032 0.001 TYR G 43 ARG 0.003 0.000 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 188 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8004 (tp) cc_final: 0.7727 (tt) REVERT: A 128 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: A 226 GLU cc_start: 0.7889 (pt0) cc_final: 0.7491 (pt0) REVERT: H 26 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.5899 (m-10) REVERT: B 171 GLU cc_start: 0.7154 (tt0) cc_final: 0.6763 (tt0) REVERT: E 281 TYR cc_start: 0.8016 (m-10) cc_final: 0.7684 (m-10) outliers start: 42 outliers final: 28 residues processed: 212 average time/residue: 0.2021 time to fit residues: 59.1363 Evaluate side-chains 199 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 173 MET Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 241 TRP Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 330 CYS Chi-restraints excluded: chain F residue 392 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 HIS ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9149 Z= 0.389 Angle : 0.780 9.737 12443 Z= 0.392 Chirality : 0.050 0.349 1510 Planarity : 0.005 0.061 1519 Dihedral : 11.696 104.279 1627 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.62 % Favored : 93.10 % Rotamer: Outliers : 4.57 % Allowed : 21.52 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -0.28 (0.27), residues: 1072 helix: 1.31 (0.31), residues: 268 sheet: -0.02 (0.28), residues: 371 loop : -1.24 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 42 HIS 0.007 0.002 HIS A 65 PHE 0.023 0.002 PHE B 148 TYR 0.028 0.002 TYR G 43 ARG 0.007 0.001 ARG G 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 173 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8460 (tp) cc_final: 0.8188 (tt) REVERT: A 128 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.7896 (m-30) REVERT: A 180 GLN cc_start: 0.8249 (mp10) cc_final: 0.8029 (mp10) REVERT: A 226 GLU cc_start: 0.7855 (pt0) cc_final: 0.7361 (pt0) REVERT: H 26 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.6280 (m-10) REVERT: H 29 ASP cc_start: 0.7377 (m-30) cc_final: 0.6766 (m-30) REVERT: B 59 LEU cc_start: 0.9107 (tp) cc_final: 0.8838 (tt) REVERT: B 83 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7464 (pm20) REVERT: B 95 TRP cc_start: 0.5589 (OUTLIER) cc_final: 0.4435 (t60) REVERT: B 111 GLU cc_start: 0.8687 (tp30) cc_final: 0.8482 (mm-30) REVERT: B 120 ARG cc_start: 0.7213 (ptp90) cc_final: 0.7004 (ptp90) REVERT: B 171 GLU cc_start: 0.7685 (tt0) cc_final: 0.7075 (tt0) REVERT: B 185 CYS cc_start: 0.6901 (t) cc_final: 0.6668 (t) REVERT: E 135 TRP cc_start: 0.8698 (m100) cc_final: 0.8236 (m-10) REVERT: E 281 TYR cc_start: 0.8367 (m-10) cc_final: 0.8037 (m-10) REVERT: F 255 TYR cc_start: 0.7749 (p90) cc_final: 0.7472 (p90) outliers start: 45 outliers final: 32 residues processed: 198 average time/residue: 0.2072 time to fit residues: 56.3914 Evaluate side-chains 199 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 163 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 173 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 241 TRP Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 392 CYS Chi-restraints excluded: chain F residue 409 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 ASN ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9149 Z= 0.228 Angle : 0.709 9.641 12443 Z= 0.353 Chirality : 0.047 0.350 1510 Planarity : 0.004 0.062 1519 Dihedral : 10.984 101.774 1627 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.50 % Favored : 94.22 % Rotamer: Outliers : 4.16 % Allowed : 22.54 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -0.30 (0.27), residues: 1072 helix: 1.23 (0.31), residues: 269 sheet: -0.00 (0.28), residues: 369 loop : -1.24 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 42 HIS 0.004 0.001 HIS E 396 PHE 0.016 0.002 PHE F 113 TYR 0.024 0.002 TYR G 43 ARG 0.007 0.001 ARG G 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 168 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8312 (tp) cc_final: 0.8051 (tt) REVERT: A 128 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: A 180 GLN cc_start: 0.8060 (mp10) cc_final: 0.7806 (mp10) REVERT: A 226 GLU cc_start: 0.7607 (pt0) cc_final: 0.7344 (pt0) REVERT: H 26 TYR cc_start: 0.7349 (OUTLIER) cc_final: 0.5939 (m-10) REVERT: H 29 ASP cc_start: 0.7417 (m-30) cc_final: 0.7083 (m-30) REVERT: B 83 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7422 (pm20) REVERT: B 95 TRP cc_start: 0.5547 (OUTLIER) cc_final: 0.4335 (t60) REVERT: B 171 GLU cc_start: 0.7570 (tt0) cc_final: 0.7196 (tt0) REVERT: B 185 CYS cc_start: 0.6825 (t) cc_final: 0.6529 (t) REVERT: E 137 MET cc_start: 0.6571 (tpt) cc_final: 0.6332 (tpt) REVERT: E 281 TYR cc_start: 0.8313 (m-10) cc_final: 0.7980 (m-10) REVERT: E 313 TYR cc_start: 0.8248 (m-80) cc_final: 0.8041 (m-10) REVERT: F 255 TYR cc_start: 0.7675 (p90) cc_final: 0.7443 (p90) outliers start: 41 outliers final: 24 residues processed: 190 average time/residue: 0.2010 time to fit residues: 53.1177 Evaluate side-chains 192 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 164 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 173 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 241 TRP Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 392 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9149 Z= 0.235 Angle : 0.715 10.511 12443 Z= 0.352 Chirality : 0.047 0.352 1510 Planarity : 0.004 0.065 1519 Dihedral : 10.662 98.776 1627 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.34 % Favored : 93.38 % Rotamer: Outliers : 4.57 % Allowed : 21.83 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -0.34 (0.27), residues: 1072 helix: 1.18 (0.31), residues: 269 sheet: 0.00 (0.28), residues: 367 loop : -1.28 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 42 HIS 0.004 0.001 HIS E 396 PHE 0.015 0.001 PHE F 113 TYR 0.025 0.002 TYR G 43 ARG 0.008 0.001 ARG G 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 168 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8331 (tp) cc_final: 0.8079 (tt) REVERT: A 128 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.7803 (m-30) REVERT: A 180 GLN cc_start: 0.8093 (mp10) cc_final: 0.7823 (mp10) REVERT: A 226 GLU cc_start: 0.7668 (pt0) cc_final: 0.7335 (pt0) REVERT: H 26 TYR cc_start: 0.7362 (OUTLIER) cc_final: 0.5807 (m-10) REVERT: H 29 ASP cc_start: 0.7431 (m-30) cc_final: 0.7079 (m-30) REVERT: B 83 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7393 (pm20) REVERT: B 95 TRP cc_start: 0.5430 (OUTLIER) cc_final: 0.4252 (t60) REVERT: B 120 ARG cc_start: 0.7423 (mtt90) cc_final: 0.7182 (mtt90) REVERT: B 171 GLU cc_start: 0.7559 (tt0) cc_final: 0.7264 (tt0) REVERT: B 185 CYS cc_start: 0.6842 (t) cc_final: 0.6634 (t) REVERT: E 135 TRP cc_start: 0.8549 (m100) cc_final: 0.8317 (m-10) REVERT: E 167 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.6994 (tp) REVERT: E 281 TYR cc_start: 0.8321 (m-10) cc_final: 0.7983 (m-10) REVERT: E 319 GLU cc_start: 0.6135 (tp30) cc_final: 0.5738 (tp30) REVERT: F 255 TYR cc_start: 0.7707 (p90) cc_final: 0.7432 (p90) outliers start: 45 outliers final: 29 residues processed: 195 average time/residue: 0.2103 time to fit residues: 56.7061 Evaluate side-chains 194 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 160 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 193 TYR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 173 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 241 TRP Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 392 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 9149 Z= 0.450 Angle : 0.852 16.246 12443 Z= 0.417 Chirality : 0.052 0.337 1510 Planarity : 0.005 0.067 1519 Dihedral : 11.458 97.486 1627 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.21 % Favored : 91.51 % Rotamer: Outliers : 4.26 % Allowed : 22.74 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -0.65 (0.26), residues: 1072 helix: 0.94 (0.30), residues: 269 sheet: -0.33 (0.28), residues: 365 loop : -1.31 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 254 HIS 0.006 0.002 HIS A 65 PHE 0.018 0.002 PHE F 113 TYR 0.028 0.002 TYR G 43 ARG 0.010 0.001 ARG G 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 163 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8150 (mp10) cc_final: 0.7866 (mp10) REVERT: H 26 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.6127 (m-10) REVERT: B 83 GLU cc_start: 0.7788 (pm20) cc_final: 0.7486 (pm20) REVERT: B 95 TRP cc_start: 0.6076 (OUTLIER) cc_final: 0.4720 (t60) REVERT: B 171 GLU cc_start: 0.7587 (tt0) cc_final: 0.7177 (tt0) REVERT: E 135 TRP cc_start: 0.8667 (m100) cc_final: 0.8419 (m-10) REVERT: E 281 TYR cc_start: 0.8458 (m-10) cc_final: 0.8128 (m-10) REVERT: E 319 GLU cc_start: 0.6133 (tp30) cc_final: 0.5698 (tp30) REVERT: F 255 TYR cc_start: 0.7978 (p90) cc_final: 0.7588 (p90) outliers start: 42 outliers final: 34 residues processed: 190 average time/residue: 0.1949 time to fit residues: 51.6524 Evaluate side-chains 195 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 159 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 193 TYR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 173 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 241 TRP Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 392 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 0.0870 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 0.1980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 HIS ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9149 Z= 0.213 Angle : 0.772 15.852 12443 Z= 0.369 Chirality : 0.048 0.340 1510 Planarity : 0.004 0.063 1519 Dihedral : 10.731 96.744 1627 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.34 % Favored : 93.38 % Rotamer: Outliers : 3.25 % Allowed : 24.06 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -0.52 (0.27), residues: 1072 helix: 1.04 (0.31), residues: 272 sheet: -0.22 (0.28), residues: 369 loop : -1.28 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 254 HIS 0.004 0.001 HIS E 105 PHE 0.016 0.001 PHE F 113 TYR 0.040 0.002 TYR G 43 ARG 0.008 0.001 ARG G 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 165 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8313 (tp) cc_final: 0.8025 (tt) REVERT: A 180 GLN cc_start: 0.8017 (mp10) cc_final: 0.7722 (mp10) REVERT: H 26 TYR cc_start: 0.7363 (OUTLIER) cc_final: 0.5824 (m-10) REVERT: B 95 TRP cc_start: 0.5800 (OUTLIER) cc_final: 0.4511 (t60) REVERT: B 171 GLU cc_start: 0.7559 (tt0) cc_final: 0.7282 (tt0) REVERT: E 135 TRP cc_start: 0.8573 (m100) cc_final: 0.8136 (m-10) REVERT: E 167 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7095 (tp) REVERT: E 281 TYR cc_start: 0.8398 (m-10) cc_final: 0.8101 (m-10) REVERT: E 319 GLU cc_start: 0.6035 (tp30) cc_final: 0.5647 (tp30) REVERT: F 255 TYR cc_start: 0.7874 (p90) cc_final: 0.7505 (p90) outliers start: 32 outliers final: 24 residues processed: 183 average time/residue: 0.2019 time to fit residues: 51.5039 Evaluate side-chains 184 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 193 TYR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 173 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 241 TRP Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 392 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN B 126 ASN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 9149 Z= 0.265 Angle : 0.784 15.344 12443 Z= 0.375 Chirality : 0.049 0.338 1510 Planarity : 0.004 0.066 1519 Dihedral : 10.622 94.429 1627 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.09 % Favored : 92.63 % Rotamer: Outliers : 2.84 % Allowed : 24.57 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.27), residues: 1072 helix: 1.04 (0.30), residues: 269 sheet: -0.29 (0.28), residues: 369 loop : -1.27 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 254 HIS 0.004 0.001 HIS E 396 PHE 0.019 0.002 PHE G 33 TYR 0.031 0.002 TYR G 43 ARG 0.007 0.001 ARG B 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 164 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8412 (tp) cc_final: 0.8117 (tt) REVERT: A 180 GLN cc_start: 0.8060 (mp10) cc_final: 0.7748 (mp10) REVERT: G 45 ARG cc_start: 0.7706 (ttt180) cc_final: 0.7481 (ttm170) REVERT: H 26 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.5812 (m-10) REVERT: B 95 TRP cc_start: 0.5907 (OUTLIER) cc_final: 0.4596 (t60) REVERT: B 171 GLU cc_start: 0.7590 (tt0) cc_final: 0.7336 (tt0) REVERT: E 135 TRP cc_start: 0.8581 (m100) cc_final: 0.8098 (m-10) REVERT: E 167 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7174 (tp) REVERT: E 281 TYR cc_start: 0.8407 (m-10) cc_final: 0.8115 (m-10) REVERT: E 319 GLU cc_start: 0.6115 (tp30) cc_final: 0.5755 (tp30) REVERT: F 255 TYR cc_start: 0.7882 (p90) cc_final: 0.7512 (p90) outliers start: 28 outliers final: 25 residues processed: 180 average time/residue: 0.2010 time to fit residues: 50.3510 Evaluate side-chains 187 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 159 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 193 TYR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 173 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 241 TRP Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 392 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 86 optimal weight: 0.0040 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.159983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129400 restraints weight = 15493.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.130874 restraints weight = 9669.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.132184 restraints weight = 8010.901| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9149 Z= 0.213 Angle : 0.784 15.742 12443 Z= 0.373 Chirality : 0.048 0.333 1510 Planarity : 0.004 0.064 1519 Dihedral : 10.221 91.699 1627 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.81 % Favored : 92.91 % Rotamer: Outliers : 2.94 % Allowed : 24.87 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -0.47 (0.27), residues: 1072 helix: 1.15 (0.31), residues: 269 sheet: -0.21 (0.28), residues: 370 loop : -1.27 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 42 HIS 0.004 0.001 HIS E 396 PHE 0.015 0.001 PHE F 113 TYR 0.023 0.001 TYR G 43 ARG 0.006 0.000 ARG B 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1974.01 seconds wall clock time: 36 minutes 12.33 seconds (2172.33 seconds total)