Starting phenix.real_space_refine on Sat Aug 23 01:30:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k7t_36941/08_2025/8k7t_36941.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k7t_36941/08_2025/8k7t_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/cci-nas-00/data/ceres_data/8k7t_36941/08_2025/8k7t_36941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k7t_36941/08_2025/8k7t_36941.map" model { file = "/net/cci-nas-00/data/ceres_data/8k7t_36941/08_2025/8k7t_36941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k7t_36941/08_2025/8k7t_36941.cif" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.23, per 1000 atoms: 0.25 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 - 3.00 Amino acid : True - 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: 1.02 Conformation dependent library (CDL) restraints added in 345.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.35 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: 1.47 Time building geometry restraints manager: 1.30 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: 0.00 - 3.24: 12279 3.24 - 6.47: 141 6.47 - 9.71: 17 9.71 - 12.94: 3 12.94 - 16.18: 3 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.180 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.830 ------------------------------------------------------------------------------- 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 9184 Z= 0.262 Angle : 0.891 16.180 12536 Z= 0.469 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG E 194 TYR 0.018 0.001 TYR F 313 PHE 0.013 0.001 PHE A 207 TRP 0.016 0.001 TRP E 172 HIS 0.008 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 9149) covalent geometry : angle 0.85287 (12443) SS BOND : bond 0.00355 ( 12) SS BOND : angle 1.07058 ( 24) hydrogen bonds : bond 0.10335 ( 420) hydrogen bonds : angle 5.01032 ( 1197) link_ALPHA1-3 : bond 0.00426 ( 2) link_ALPHA1-3 : angle 1.44986 ( 6) link_ALPHA1-6 : bond 0.00472 ( 2) link_ALPHA1-6 : angle 1.51719 ( 6) link_BETA1-4 : bond 0.00868 ( 8) link_BETA1-4 : angle 1.82939 ( 24) link_NAG-ASN : bond 0.00895 ( 11) link_NAG-ASN : angle 4.81424 ( 33) *********************** 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 to be fit. rotamer outliers: 6 poor density : 252 time to evaluate : 0.352 Fit side-chains revert: symmetry clash 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: 0.6473 (m-80) REVERT: H 28 LEU cc_start: 0.8222 (tt) cc_final: 0.7978 (tt) REVERT: B 123 LEU cc_start: 0.8378 (tp) cc_final: 0.7913 (tt) REVERT: E 135 TRP cc_start: 0.8321 (m100) cc_final: 0.7797 (m-10) outliers start: 6 outliers final: 2 residues processed: 257 average time/residue: 0.0994 time to fit residues: 35.2251 Evaluate side-chains 193 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 49 optimal weight: 9.9990 chunk 97 optimal weight: 0.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 204 GLN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.167747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.137245 restraints weight = 15565.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.141169 restraints weight = 9645.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.142253 restraints weight = 6690.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.142095 restraints weight = 5091.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.142357 restraints weight = 5280.613| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9184 Z= 0.198 Angle : 0.795 10.231 12536 Z= 0.378 Chirality : 0.048 0.326 1510 Planarity : 0.005 0.057 1519 Dihedral : 13.973 110.680 1631 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.60 % Favored : 94.03 % Rotamer: Outliers : 3.96 % Allowed : 17.46 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.26), residues: 1072 helix: 1.66 (0.30), residues: 260 sheet: 0.19 (0.27), residues: 383 loop : -1.19 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 45 TYR 0.022 0.002 TYR B 193 PHE 0.023 0.002 PHE E 335 TRP 0.020 0.002 TRP B 42 HIS 0.004 0.001 HIS E 396 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 9149) covalent geometry : angle 0.74231 (12443) SS BOND : bond 0.00920 ( 12) SS BOND : angle 1.53070 ( 24) hydrogen bonds : bond 0.04088 ( 420) hydrogen bonds : angle 4.54334 ( 1197) link_ALPHA1-3 : bond 0.01090 ( 2) link_ALPHA1-3 : angle 2.31749 ( 6) link_ALPHA1-6 : bond 0.00375 ( 2) link_ALPHA1-6 : angle 2.43430 ( 6) link_BETA1-4 : bond 0.00522 ( 8) link_BETA1-4 : angle 2.86269 ( 24) link_NAG-ASN : bond 0.00743 ( 11) link_NAG-ASN : angle 4.77883 ( 33) *********************** 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 231 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 THR cc_start: 0.7661 (OUTLIER) cc_final: 0.7346 (t) REVERT: G 29 ASP cc_start: 0.7302 (t0) cc_final: 0.7030 (t0) REVERT: H 26 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.6511 (m-80) REVERT: B 81 ASP cc_start: 0.8844 (p0) cc_final: 0.8375 (p0) REVERT: B 83 GLU cc_start: 0.7804 (pm20) cc_final: 0.7467 (pm20) REVERT: E 296 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7964 (pt) REVERT: E 345 LEU cc_start: 0.7912 (mp) cc_final: 0.7583 (tp) outliers start: 39 outliers final: 20 residues processed: 218 average time/residue: 0.0897 time to fit residues: 27.1836 Evaluate side-chains 192 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 128 ASP Chi-restraints excluded: chain A residue 148 ASP 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 204 VAL 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 258 HIS Chi-restraints excluded: chain F residue 392 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 34 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 105 HIS ** 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 F 393 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.165097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.134177 restraints weight = 15511.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.137116 restraints weight = 10399.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.138795 restraints weight = 7122.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.138705 restraints weight = 5396.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.139398 restraints weight = 5660.156| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9184 Z= 0.170 Angle : 0.733 8.678 12536 Z= 0.355 Chirality : 0.048 0.352 1510 Planarity : 0.004 0.057 1519 Dihedral : 12.337 108.863 1627 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.78 % Favored : 93.84 % Rotamer: Outliers : 4.16 % Allowed : 18.48 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.26), residues: 1072 helix: 1.70 (0.30), residues: 261 sheet: 0.06 (0.27), residues: 378 loop : -1.15 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 58 TYR 0.033 0.002 TYR G 43 PHE 0.022 0.002 PHE B 148 TRP 0.011 0.001 TRP E 135 HIS 0.006 0.001 HIS E 396 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 9149) covalent geometry : angle 0.68737 (12443) SS BOND : bond 0.00352 ( 12) SS BOND : angle 1.31351 ( 24) hydrogen bonds : bond 0.04049 ( 420) hydrogen bonds : angle 4.52691 ( 1197) link_ALPHA1-3 : bond 0.01070 ( 2) link_ALPHA1-3 : angle 1.44011 ( 6) link_ALPHA1-6 : bond 0.00326 ( 2) link_ALPHA1-6 : angle 2.59037 ( 6) link_BETA1-4 : bond 0.00486 ( 8) link_BETA1-4 : angle 2.45814 ( 24) link_NAG-ASN : bond 0.00747 ( 11) link_NAG-ASN : angle 4.31343 ( 33) *********************** 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 226 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8406 (mptt) REVERT: A 114 LEU cc_start: 0.8428 (tp) cc_final: 0.8056 (tt) REVERT: A 128 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7732 (m-30) REVERT: A 226 GLU cc_start: 0.8533 (pt0) cc_final: 0.8017 (pp20) REVERT: H 26 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.6261 (m-10) REVERT: B 81 ASP cc_start: 0.8929 (p0) cc_final: 0.8486 (p0) REVERT: B 83 GLU cc_start: 0.7792 (pm20) cc_final: 0.7480 (pm20) REVERT: B 95 TRP cc_start: 0.5500 (t60) cc_final: 0.4146 (t60) REVERT: B 171 GLU cc_start: 0.7501 (tt0) cc_final: 0.7155 (tt0) REVERT: B 185 CYS cc_start: 0.7766 (t) cc_final: 0.7421 (t) REVERT: E 296 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7972 (pt) REVERT: F 111 ASN cc_start: 0.8444 (m-40) cc_final: 0.8240 (m-40) REVERT: F 255 TYR cc_start: 0.7515 (p90) cc_final: 0.7082 (p90) REVERT: F 362 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6535 (mp) outliers start: 41 outliers final: 26 residues processed: 208 average time/residue: 0.0875 time to fit residues: 25.3130 Evaluate side-chains 195 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 221 LEU 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 64 CYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 75 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 E residue 314 VAL Chi-restraints excluded: chain F residue 114 HIS 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 330 CYS Chi-restraints excluded: chain F residue 362 LEU 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 5 optimal weight: 0.0470 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 18 optimal weight: 0.2980 chunk 83 optimal weight: 0.8980 chunk 94 optimal weight: 0.4980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 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 289 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.166356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.135073 restraints weight = 15677.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.138223 restraints weight = 10884.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.139658 restraints weight = 7227.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.139994 restraints weight = 5472.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.140370 restraints weight = 5255.165| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9184 Z= 0.131 Angle : 0.711 13.298 12536 Z= 0.339 Chirality : 0.047 0.361 1510 Planarity : 0.004 0.060 1519 Dihedral : 11.128 105.546 1627 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.60 % Favored : 94.12 % Rotamer: Outliers : 4.06 % Allowed : 21.12 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.26), residues: 1072 helix: 1.70 (0.31), residues: 261 sheet: 0.16 (0.28), residues: 375 loop : -1.20 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 179 TYR 0.018 0.001 TYR G 43 PHE 0.022 0.002 PHE B 148 TRP 0.018 0.001 TRP B 42 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9149) covalent geometry : angle 0.67178 (12443) SS BOND : bond 0.00334 ( 12) SS BOND : angle 1.03405 ( 24) hydrogen bonds : bond 0.03913 ( 420) hydrogen bonds : angle 4.44403 ( 1197) link_ALPHA1-3 : bond 0.01192 ( 2) link_ALPHA1-3 : angle 1.58091 ( 6) link_ALPHA1-6 : bond 0.00578 ( 2) link_ALPHA1-6 : angle 2.35969 ( 6) link_BETA1-4 : bond 0.00487 ( 8) link_BETA1-4 : angle 2.48763 ( 24) link_NAG-ASN : bond 0.00741 ( 11) link_NAG-ASN : angle 3.86978 ( 33) *********************** 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 220 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8680 (mtpp) cc_final: 0.8379 (mptt) REVERT: A 114 LEU cc_start: 0.8405 (tp) cc_final: 0.8113 (tt) REVERT: A 226 GLU cc_start: 0.8439 (pt0) cc_final: 0.7825 (pt0) REVERT: H 26 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.6024 (m-10) REVERT: B 81 ASP cc_start: 0.8923 (p0) cc_final: 0.8502 (p0) REVERT: B 83 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: B 111 GLU cc_start: 0.8780 (tp30) cc_final: 0.7789 (tp30) REVERT: B 120 ARG cc_start: 0.7541 (mtt90) cc_final: 0.7310 (ptp90) REVERT: B 171 GLU cc_start: 0.7702 (tt0) cc_final: 0.7261 (tt0) REVERT: B 185 CYS cc_start: 0.7544 (t) cc_final: 0.7170 (t) REVERT: F 255 TYR cc_start: 0.7469 (p90) cc_final: 0.7072 (p90) outliers start: 40 outliers final: 22 residues processed: 203 average time/residue: 0.0941 time to fit residues: 26.3756 Evaluate side-chains 194 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 201 TYR 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 90 LEU 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 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 314 VAL Chi-restraints excluded: chain E residue 375 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 241 TRP 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 50 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.163487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.133115 restraints weight = 15547.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.134150 restraints weight = 9739.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.135527 restraints weight = 8222.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.136251 restraints weight = 6528.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.136589 restraints weight = 6287.835| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9184 Z= 0.159 Angle : 0.744 14.472 12536 Z= 0.354 Chirality : 0.047 0.359 1510 Planarity : 0.004 0.061 1519 Dihedral : 10.951 102.879 1627 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.16 % Favored : 93.56 % Rotamer: Outliers : 4.37 % Allowed : 21.52 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.27), residues: 1072 helix: 1.55 (0.31), residues: 267 sheet: 0.09 (0.28), residues: 374 loop : -1.26 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 43 TYR 0.022 0.002 TYR G 43 PHE 0.014 0.002 PHE E 335 TRP 0.034 0.001 TRP B 42 HIS 0.004 0.001 HIS E 396 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 9149) covalent geometry : angle 0.70692 (12443) SS BOND : bond 0.00331 ( 12) SS BOND : angle 1.15001 ( 24) hydrogen bonds : bond 0.03985 ( 420) hydrogen bonds : angle 4.47509 ( 1197) link_ALPHA1-3 : bond 0.00972 ( 2) link_ALPHA1-3 : angle 1.48331 ( 6) link_ALPHA1-6 : bond 0.00428 ( 2) link_ALPHA1-6 : angle 2.60578 ( 6) link_BETA1-4 : bond 0.00442 ( 8) link_BETA1-4 : angle 2.39898 ( 24) link_NAG-ASN : bond 0.00709 ( 11) link_NAG-ASN : angle 3.85323 ( 33) *********************** 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 222 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8703 (mtpp) cc_final: 0.8384 (mptt) REVERT: A 114 LEU cc_start: 0.8529 (tp) cc_final: 0.8239 (tt) REVERT: A 226 GLU cc_start: 0.8524 (pt0) cc_final: 0.7912 (pt0) REVERT: H 26 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.6020 (m-10) REVERT: B 81 ASP cc_start: 0.8954 (p0) cc_final: 0.8538 (p0) REVERT: B 83 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7710 (pm20) REVERT: B 95 TRP cc_start: 0.5577 (OUTLIER) cc_final: 0.3957 (t60) REVERT: B 171 GLU cc_start: 0.7865 (tt0) cc_final: 0.7474 (tt0) REVERT: B 185 CYS cc_start: 0.7711 (t) cc_final: 0.7412 (t) REVERT: E 135 TRP cc_start: 0.8516 (m100) cc_final: 0.8258 (m-10) REVERT: F 255 TYR cc_start: 0.7620 (p90) cc_final: 0.7283 (p90) REVERT: F 362 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6432 (mp) outliers start: 43 outliers final: 32 residues processed: 205 average time/residue: 0.0922 time to fit residues: 26.4085 Evaluate side-chains 209 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 221 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 95 TRP Chi-restraints excluded: chain B residue 106 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 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 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 208 LEU Chi-restraints excluded: chain F residue 241 TRP Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 392 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 0.0050 chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.1400 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.155791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.125784 restraints weight = 15712.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.125997 restraints weight = 10138.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.127204 restraints weight = 10632.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.127921 restraints weight = 7292.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128317 restraints weight = 6673.574| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 9184 Z= 0.269 Angle : 0.847 14.800 12536 Z= 0.408 Chirality : 0.050 0.346 1510 Planarity : 0.005 0.065 1519 Dihedral : 11.672 101.579 1627 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.37 % Favored : 92.35 % Rotamer: Outliers : 5.48 % Allowed : 21.62 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.26), residues: 1072 helix: 1.19 (0.30), residues: 269 sheet: -0.16 (0.28), residues: 370 loop : -1.30 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 43 TYR 0.024 0.002 TYR G 43 PHE 0.017 0.002 PHE F 113 TRP 0.018 0.002 TRP B 42 HIS 0.006 0.002 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00631 ( 9149) covalent geometry : angle 0.80543 (12443) SS BOND : bond 0.00496 ( 12) SS BOND : angle 1.63887 ( 24) hydrogen bonds : bond 0.04480 ( 420) hydrogen bonds : angle 4.80926 ( 1197) link_ALPHA1-3 : bond 0.00817 ( 2) link_ALPHA1-3 : angle 1.58311 ( 6) link_ALPHA1-6 : bond 0.00110 ( 2) link_ALPHA1-6 : angle 3.06319 ( 6) link_BETA1-4 : bond 0.00554 ( 8) link_BETA1-4 : angle 2.62655 ( 24) link_NAG-ASN : bond 0.00692 ( 11) link_NAG-ASN : angle 4.30534 ( 33) *********************** 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 229 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 175 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8750 (mtpp) cc_final: 0.8413 (mtmt) REVERT: A 114 LEU cc_start: 0.8834 (tp) cc_final: 0.8519 (tt) REVERT: A 128 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: A 180 GLN cc_start: 0.8401 (mp10) cc_final: 0.8139 (mp10) REVERT: A 226 GLU cc_start: 0.8214 (pt0) cc_final: 0.7745 (pt0) REVERT: H 26 TYR cc_start: 0.7664 (OUTLIER) cc_final: 0.6249 (m-10) REVERT: B 95 TRP cc_start: 0.6168 (OUTLIER) cc_final: 0.4922 (t60) REVERT: B 171 GLU cc_start: 0.7707 (tt0) cc_final: 0.7355 (tt0) REVERT: B 185 CYS cc_start: 0.7558 (t) cc_final: 0.7257 (t) REVERT: E 118 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6935 (mm-40) REVERT: F 255 TYR cc_start: 0.7693 (p90) cc_final: 0.7402 (p90) REVERT: F 362 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6782 (mp) outliers start: 54 outliers final: 35 residues processed: 212 average time/residue: 0.0886 time to fit residues: 26.3901 Evaluate side-chains 201 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 27 ILE 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 95 TRP Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 135 THR 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 E residue 103 LEU Chi-restraints excluded: chain E residue 118 GLN 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 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 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 208 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 241 TRP 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 362 LEU Chi-restraints excluded: chain F residue 392 CYS Chi-restraints excluded: chain F residue 409 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 170 GLN ** 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 365 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.159770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129585 restraints weight = 15695.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.129823 restraints weight = 9793.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.131283 restraints weight = 9021.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.131918 restraints weight = 7033.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.132041 restraints weight = 6681.191| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9184 Z= 0.150 Angle : 0.776 13.570 12536 Z= 0.369 Chirality : 0.048 0.347 1510 Planarity : 0.004 0.062 1519 Dihedral : 10.856 99.210 1627 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.06 % Favored : 93.66 % Rotamer: Outliers : 3.86 % Allowed : 23.86 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.26), residues: 1072 helix: 1.22 (0.30), residues: 269 sheet: -0.16 (0.28), residues: 369 loop : -1.27 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 43 TYR 0.024 0.002 TYR G 43 PHE 0.014 0.002 PHE F 113 TRP 0.031 0.002 TRP E 135 HIS 0.004 0.001 HIS E 396 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9149) covalent geometry : angle 0.74382 (12443) SS BOND : bond 0.00361 ( 12) SS BOND : angle 1.21535 ( 24) hydrogen bonds : bond 0.04114 ( 420) hydrogen bonds : angle 4.67555 ( 1197) link_ALPHA1-3 : bond 0.01100 ( 2) link_ALPHA1-3 : angle 1.32642 ( 6) link_ALPHA1-6 : bond 0.00530 ( 2) link_ALPHA1-6 : angle 2.57010 ( 6) link_BETA1-4 : bond 0.00478 ( 8) link_BETA1-4 : angle 2.26005 ( 24) link_NAG-ASN : bond 0.00710 ( 11) link_NAG-ASN : angle 3.74773 ( 33) *********************** 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 217 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8711 (mtpp) cc_final: 0.8367 (mtmt) REVERT: A 114 LEU cc_start: 0.8653 (tp) cc_final: 0.8388 (tt) REVERT: A 128 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.7962 (m-30) REVERT: A 180 GLN cc_start: 0.8200 (mp10) cc_final: 0.7928 (mp10) REVERT: A 226 GLU cc_start: 0.8276 (pt0) cc_final: 0.7877 (pp20) REVERT: A 229 PHE cc_start: 0.7965 (t80) cc_final: 0.7710 (t80) REVERT: G 46 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8688 (mm) REVERT: G 47 LYS cc_start: 0.8897 (tptp) cc_final: 0.8693 (pttt) REVERT: G 52 LYS cc_start: 0.8352 (ttpp) cc_final: 0.8029 (pttm) REVERT: H 26 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.6301 (m-10) REVERT: H 29 ASP cc_start: 0.8357 (m-30) cc_final: 0.8031 (m-30) REVERT: B 81 ASP cc_start: 0.8725 (p0) cc_final: 0.8256 (p0) REVERT: B 83 GLU cc_start: 0.7690 (pm20) cc_final: 0.7223 (pm20) REVERT: B 95 TRP cc_start: 0.6047 (OUTLIER) cc_final: 0.4521 (t60) REVERT: B 123 LEU cc_start: 0.8995 (pp) cc_final: 0.8674 (tt) REVERT: B 171 GLU cc_start: 0.7759 (tt0) cc_final: 0.7518 (tt0) REVERT: B 180 THR cc_start: 0.9024 (m) cc_final: 0.8811 (m) REVERT: B 185 CYS cc_start: 0.7475 (t) cc_final: 0.7153 (t) REVERT: E 118 GLN cc_start: 0.6744 (OUTLIER) cc_final: 0.6154 (mm-40) REVERT: F 255 TYR cc_start: 0.7688 (p90) cc_final: 0.7387 (p90) outliers start: 38 outliers final: 23 residues processed: 201 average time/residue: 0.0940 time to fit residues: 26.2852 Evaluate side-chains 192 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 39 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 95 TRP Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 LEU 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 118 GLN Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 228 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 208 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 77 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 78 optimal weight: 0.0770 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 0.0070 chunk 76 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 overall best weight: 0.5556 ------------------------------------------------------------------------------- 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 204 GLN ** 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 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 = 0.4098 r_free = 0.4098 target = 0.160479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130287 restraints weight = 15542.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.130150 restraints weight = 9873.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.131144 restraints weight = 8989.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.132067 restraints weight = 7449.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.132317 restraints weight = 7022.377| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9184 Z= 0.142 Angle : 0.780 17.326 12536 Z= 0.367 Chirality : 0.048 0.347 1510 Planarity : 0.004 0.066 1519 Dihedral : 10.341 95.530 1627 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.90 % Favored : 92.82 % Rotamer: Outliers : 4.06 % Allowed : 23.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.26), residues: 1072 helix: 1.23 (0.30), residues: 269 sheet: -0.12 (0.28), residues: 368 loop : -1.25 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 43 TYR 0.022 0.001 TYR G 43 PHE 0.019 0.001 PHE E 178 TRP 0.027 0.001 TRP E 135 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9149) covalent geometry : angle 0.75148 (12443) SS BOND : bond 0.00545 ( 12) SS BOND : angle 1.07212 ( 24) hydrogen bonds : bond 0.04130 ( 420) hydrogen bonds : angle 4.59211 ( 1197) link_ALPHA1-3 : bond 0.01029 ( 2) link_ALPHA1-3 : angle 1.43726 ( 6) link_ALPHA1-6 : bond 0.00625 ( 2) link_ALPHA1-6 : angle 2.44997 ( 6) link_BETA1-4 : bond 0.00487 ( 8) link_BETA1-4 : angle 2.22008 ( 24) link_NAG-ASN : bond 0.00651 ( 11) link_NAG-ASN : angle 3.51776 ( 33) *********************** 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 209 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8636 (tp) cc_final: 0.8407 (tt) REVERT: A 128 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.7914 (m-30) REVERT: A 180 GLN cc_start: 0.8184 (mp10) cc_final: 0.7893 (mp10) REVERT: A 226 GLU cc_start: 0.8232 (pt0) cc_final: 0.7806 (pp20) REVERT: G 47 LYS cc_start: 0.8907 (tptp) cc_final: 0.8659 (pttt) REVERT: G 49 GLN cc_start: 0.8352 (pt0) cc_final: 0.7949 (pt0) REVERT: G 52 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7948 (pttp) REVERT: H 26 TYR cc_start: 0.7581 (OUTLIER) cc_final: 0.6155 (m-10) REVERT: H 29 ASP cc_start: 0.8363 (m-30) cc_final: 0.7992 (m-30) REVERT: B 95 TRP cc_start: 0.6051 (OUTLIER) cc_final: 0.4449 (t60) REVERT: B 123 LEU cc_start: 0.8973 (pp) cc_final: 0.8677 (tt) REVERT: B 185 CYS cc_start: 0.7429 (t) cc_final: 0.7212 (t) REVERT: E 118 GLN cc_start: 0.6796 (OUTLIER) cc_final: 0.6459 (mm-40) REVERT: E 319 GLU cc_start: 0.6132 (tp30) cc_final: 0.5728 (tp30) REVERT: F 104 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7270 (mt) REVERT: F 255 TYR cc_start: 0.7645 (p90) cc_final: 0.7348 (p90) REVERT: F 362 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6492 (mp) outliers start: 40 outliers final: 25 residues processed: 195 average time/residue: 0.0914 time to fit residues: 25.0432 Evaluate side-chains 188 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 H residue 26 TYR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 106 LEU 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 118 GLN Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 104 LEU 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 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 269 ILE Chi-restraints excluded: chain F residue 362 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 83 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 88 optimal weight: 0.4980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 204 GLN ** 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 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 = 0.4078 r_free = 0.4078 target = 0.158526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.128331 restraints weight = 15569.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.128499 restraints weight = 9959.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.129357 restraints weight = 9066.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.130419 restraints weight = 7577.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.130833 restraints weight = 6587.949| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9184 Z= 0.163 Angle : 0.811 17.355 12536 Z= 0.377 Chirality : 0.048 0.334 1510 Planarity : 0.004 0.066 1519 Dihedral : 10.291 92.287 1627 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.09 % Favored : 92.63 % Rotamer: Outliers : 3.35 % Allowed : 23.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.26), residues: 1072 helix: 1.16 (0.30), residues: 269 sheet: -0.14 (0.28), residues: 369 loop : -1.23 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 43 TYR 0.031 0.002 TYR G 43 PHE 0.017 0.001 PHE E 178 TRP 0.025 0.002 TRP E 135 HIS 0.004 0.001 HIS E 396 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 9149) covalent geometry : angle 0.78147 (12443) SS BOND : bond 0.00510 ( 12) SS BOND : angle 1.20321 ( 24) hydrogen bonds : bond 0.04208 ( 420) hydrogen bonds : angle 4.65503 ( 1197) link_ALPHA1-3 : bond 0.00998 ( 2) link_ALPHA1-3 : angle 1.43853 ( 6) link_ALPHA1-6 : bond 0.00504 ( 2) link_ALPHA1-6 : angle 2.59100 ( 6) link_BETA1-4 : bond 0.00460 ( 8) link_BETA1-4 : angle 2.22137 ( 24) link_NAG-ASN : bond 0.00580 ( 11) link_NAG-ASN : angle 3.67899 ( 33) *********************** 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 196 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8634 (tp) cc_final: 0.8374 (tt) REVERT: A 128 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.7920 (m-30) REVERT: A 180 GLN cc_start: 0.8162 (mp10) cc_final: 0.7854 (mp10) REVERT: A 226 GLU cc_start: 0.8229 (pt0) cc_final: 0.7842 (pt0) REVERT: G 49 GLN cc_start: 0.8168 (pt0) cc_final: 0.7801 (pt0) REVERT: G 52 LYS cc_start: 0.8108 (ttpp) cc_final: 0.7888 (pttp) REVERT: H 26 TYR cc_start: 0.7526 (OUTLIER) cc_final: 0.6188 (m-10) REVERT: H 29 ASP cc_start: 0.8441 (m-30) cc_final: 0.8110 (m-30) REVERT: B 83 GLU cc_start: 0.7630 (pm20) cc_final: 0.7266 (pm20) REVERT: B 95 TRP cc_start: 0.5893 (OUTLIER) cc_final: 0.4558 (t60) REVERT: B 123 LEU cc_start: 0.8986 (pp) cc_final: 0.8679 (tt) REVERT: B 185 CYS cc_start: 0.7656 (t) cc_final: 0.7413 (t) REVERT: E 118 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.6488 (mm-40) REVERT: E 319 GLU cc_start: 0.6263 (tp30) cc_final: 0.5879 (tp30) REVERT: F 255 TYR cc_start: 0.7717 (p90) cc_final: 0.7409 (p90) REVERT: F 362 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6580 (mp) outliers start: 33 outliers final: 26 residues processed: 182 average time/residue: 0.0977 time to fit residues: 24.6422 Evaluate side-chains 188 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 39 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 95 TRP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 193 TYR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 118 GLN Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 228 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 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 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 269 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 87 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 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** A 65 HIS ** 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 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 = 0.4084 r_free = 0.4084 target = 0.158975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.128661 restraints weight = 15666.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.130628 restraints weight = 9885.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.131925 restraints weight = 8004.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.132235 restraints weight = 5923.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.132380 restraints weight = 5910.144| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 9184 Z= 0.159 Angle : 0.814 17.950 12536 Z= 0.378 Chirality : 0.048 0.327 1510 Planarity : 0.004 0.065 1519 Dihedral : 10.121 89.757 1627 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.00 % Favored : 92.72 % Rotamer: Outliers : 3.35 % Allowed : 24.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.27), residues: 1072 helix: 1.32 (0.30), residues: 278 sheet: -0.13 (0.28), residues: 371 loop : -1.23 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 43 TYR 0.012 0.001 TYR B 193 PHE 0.020 0.001 PHE E 178 TRP 0.028 0.002 TRP E 135 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9149) covalent geometry : angle 0.78644 (12443) SS BOND : bond 0.00488 ( 12) SS BOND : angle 1.13113 ( 24) hydrogen bonds : bond 0.04206 ( 420) hydrogen bonds : angle 4.63568 ( 1197) link_ALPHA1-3 : bond 0.00985 ( 2) link_ALPHA1-3 : angle 1.37753 ( 6) link_ALPHA1-6 : bond 0.00612 ( 2) link_ALPHA1-6 : angle 2.60401 ( 6) link_BETA1-4 : bond 0.00465 ( 8) link_BETA1-4 : angle 2.12341 ( 24) link_NAG-ASN : bond 0.00605 ( 11) link_NAG-ASN : angle 3.58709 ( 33) ********************** 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 199 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8680 (tp) cc_final: 0.8414 (tt) REVERT: A 180 GLN cc_start: 0.8191 (mp10) cc_final: 0.7864 (mp10) REVERT: A 226 GLU cc_start: 0.8180 (pt0) cc_final: 0.7903 (pt0) REVERT: G 49 GLN cc_start: 0.8178 (pt0) cc_final: 0.7785 (pt0) REVERT: H 26 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6072 (m-10) REVERT: H 29 ASP cc_start: 0.8511 (m-30) cc_final: 0.8164 (m-30) REVERT: B 83 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7285 (pm20) REVERT: B 95 TRP cc_start: 0.6107 (OUTLIER) cc_final: 0.4653 (t60) REVERT: B 120 ARG cc_start: 0.7525 (mtt90) cc_final: 0.7165 (mtt90) REVERT: B 123 LEU cc_start: 0.8965 (pp) cc_final: 0.8680 (tt) REVERT: E 118 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6596 (mm-40) REVERT: E 319 GLU cc_start: 0.6271 (tp30) cc_final: 0.5855 (tp30) REVERT: F 255 TYR cc_start: 0.7775 (p90) cc_final: 0.7457 (p90) REVERT: F 362 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6585 (mp) outliers start: 33 outliers final: 27 residues processed: 186 average time/residue: 0.0890 time to fit residues: 22.9068 Evaluate side-chains 192 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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 106 LEU 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 118 GLN Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 228 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 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 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 269 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 39 optimal weight: 7.9990 chunk 94 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 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 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.159453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.129141 restraints weight = 15470.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.130038 restraints weight = 9781.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.132273 restraints weight = 8319.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.132635 restraints weight = 6323.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.133687 restraints weight = 6410.202| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9184 Z= 0.147 Angle : 0.809 18.262 12536 Z= 0.377 Chirality : 0.048 0.342 1510 Planarity : 0.004 0.065 1519 Dihedral : 9.909 85.741 1627 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.81 % Favored : 92.91 % Rotamer: Outliers : 3.55 % Allowed : 24.47 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.27), residues: 1072 helix: 1.26 (0.30), residues: 275 sheet: -0.09 (0.28), residues: 371 loop : -1.25 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 43 TYR 0.025 0.002 TYR G 26 PHE 0.018 0.001 PHE E 178 TRP 0.025 0.001 TRP E 135 HIS 0.004 0.001 HIS E 396 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9149) covalent geometry : angle 0.78207 (12443) SS BOND : bond 0.00488 ( 12) SS BOND : angle 1.08604 ( 24) hydrogen bonds : bond 0.04222 ( 420) hydrogen bonds : angle 4.62555 ( 1197) link_ALPHA1-3 : bond 0.01082 ( 2) link_ALPHA1-3 : angle 1.45266 ( 6) link_ALPHA1-6 : bond 0.00630 ( 2) link_ALPHA1-6 : angle 2.47434 ( 6) link_BETA1-4 : bond 0.00506 ( 8) link_BETA1-4 : angle 2.07998 ( 24) link_NAG-ASN : bond 0.00607 ( 11) link_NAG-ASN : angle 3.54772 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1479.68 seconds wall clock time: 26 minutes 23.93 seconds (1583.93 seconds total)