Starting phenix.real_space_refine on Thu May 15 09:36:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tul_41624/05_2025/8tul_41624.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tul_41624/05_2025/8tul_41624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tul_41624/05_2025/8tul_41624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tul_41624/05_2025/8tul_41624.map" model { file = "/net/cci-nas-00/data/ceres_data/8tul_41624/05_2025/8tul_41624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tul_41624/05_2025/8tul_41624.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.268 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 14 5.21 5 S 65 5.16 5 C 8195 2.51 5 N 2150 2.21 5 O 2646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13070 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2555 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 309} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Restraints were copied for chains: B, C, D, E Time building chain proxies: 6.59, per 1000 atoms: 0.50 Number of scatterers: 13070 At special positions: 0 Unit cell: (106.24, 107.07, 140.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 Mg 14 11.99 O 2646 8.00 N 2150 7.00 C 8195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.6 seconds 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3020 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 68.1% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.675A pdb=" N GLN A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.754A pdb=" N GLY A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 219 Proline residue: A 209 - end of helix removed outlier: 3.607A pdb=" N ALA A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 261 removed outlier: 3.533A pdb=" N LEU A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 268 removed outlier: 3.633A pdb=" N LEU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 removed outlier: 3.610A pdb=" N TRP A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.026A pdb=" N SER A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 359 removed outlier: 3.535A pdb=" N TYR A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 399 removed outlier: 3.509A pdb=" N LEU A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 112 removed outlier: 3.676A pdb=" N GLN B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.754A pdb=" N GLY B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 219 Proline residue: B 209 - end of helix removed outlier: 3.607A pdb=" N ALA B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 261 removed outlier: 3.533A pdb=" N LEU B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 268 removed outlier: 3.632A pdb=" N LEU B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 removed outlier: 3.610A pdb=" N TRP B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 removed outlier: 4.026A pdb=" N SER B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 359 removed outlier: 3.535A pdb=" N TYR B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY B 356 " --> pdb=" O PHE B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 399 removed outlier: 3.509A pdb=" N LEU B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 112 removed outlier: 3.675A pdb=" N GLN C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 165 Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.754A pdb=" N GLY C 173 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 219 Proline residue: C 209 - end of helix removed outlier: 3.607A pdb=" N ALA C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 261 removed outlier: 3.533A pdb=" N LEU C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 268 removed outlier: 3.632A pdb=" N LEU C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 removed outlier: 3.610A pdb=" N TRP C 273 " --> pdb=" O CYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 removed outlier: 4.027A pdb=" N SER C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 359 removed outlier: 3.535A pdb=" N TYR C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 333 " --> pdb=" O ASP C 329 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY C 356 " --> pdb=" O PHE C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 399 removed outlier: 3.509A pdb=" N LEU C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 112 removed outlier: 3.675A pdb=" N GLN D 109 " --> pdb=" O THR D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 165 Processing helix chain 'D' and resid 166 through 173 removed outlier: 3.755A pdb=" N GLY D 173 " --> pdb=" O SER D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 219 Proline residue: D 209 - end of helix removed outlier: 3.607A pdb=" N ALA D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 261 removed outlier: 3.533A pdb=" N LEU D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 268 removed outlier: 3.632A pdb=" N LEU D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 removed outlier: 3.610A pdb=" N TRP D 273 " --> pdb=" O CYS D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 282 removed outlier: 4.026A pdb=" N SER D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 359 removed outlier: 3.536A pdb=" N TYR D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN D 333 " --> pdb=" O ASP D 329 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY D 356 " --> pdb=" O PHE D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 399 removed outlier: 3.509A pdb=" N LEU D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 112 removed outlier: 3.676A pdb=" N GLN E 109 " --> pdb=" O THR E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.754A pdb=" N GLY E 173 " --> pdb=" O SER E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 219 Proline residue: E 209 - end of helix removed outlier: 3.608A pdb=" N ALA E 217 " --> pdb=" O GLU E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 261 removed outlier: 3.533A pdb=" N LEU E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE E 233 " --> pdb=" O SER E 229 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 268 removed outlier: 3.632A pdb=" N LEU E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 275 removed outlier: 3.610A pdb=" N TRP E 273 " --> pdb=" O CYS E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.026A pdb=" N SER E 282 " --> pdb=" O VAL E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 359 removed outlier: 3.535A pdb=" N TYR E 299 " --> pdb=" O LEU E 295 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN E 333 " --> pdb=" O ASP E 329 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N MET E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY E 356 " --> pdb=" O PHE E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 399 removed outlier: 3.509A pdb=" N LEU E 396 " --> pdb=" O LEU E 392 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 102 removed outlier: 4.014A pdb=" N LYS A 141 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 102 removed outlier: 4.013A pdb=" N LYS B 141 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 102 removed outlier: 4.014A pdb=" N LYS C 141 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 97 through 102 removed outlier: 4.014A pdb=" N LYS D 141 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 102 removed outlier: 4.014A pdb=" N LYS E 141 " --> pdb=" O LEU E 152 " (cutoff:3.500A) 900 hydrogen bonds defined for protein. 2640 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: 4.38 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3259 1.33 - 1.45: 2212 1.45 - 1.57: 7409 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 13000 Sorted by residual: bond pdb=" C MET D 336 " pdb=" O MET D 336 " ideal model delta sigma weight residual 1.236 1.214 0.022 1.29e-02 6.01e+03 3.03e+00 bond pdb=" C MET E 336 " pdb=" O MET E 336 " ideal model delta sigma weight residual 1.236 1.215 0.022 1.29e-02 6.01e+03 2.80e+00 bond pdb=" C MET C 336 " pdb=" O MET C 336 " ideal model delta sigma weight residual 1.236 1.215 0.021 1.29e-02 6.01e+03 2.75e+00 bond pdb=" C MET B 336 " pdb=" O MET B 336 " ideal model delta sigma weight residual 1.236 1.215 0.021 1.29e-02 6.01e+03 2.75e+00 bond pdb=" C MET A 336 " pdb=" O MET A 336 " ideal model delta sigma weight residual 1.236 1.215 0.021 1.29e-02 6.01e+03 2.72e+00 ... (remaining 12995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 17151 1.34 - 2.68: 344 2.68 - 4.02: 32 4.02 - 5.36: 18 5.36 - 6.70: 10 Bond angle restraints: 17555 Sorted by residual: angle pdb=" N GLY C 353 " pdb=" CA GLY C 353 " pdb=" C GLY C 353 " ideal model delta sigma weight residual 115.32 111.27 4.05 1.31e+00 5.83e-01 9.56e+00 angle pdb=" N GLY B 353 " pdb=" CA GLY B 353 " pdb=" C GLY B 353 " ideal model delta sigma weight residual 115.32 111.27 4.05 1.31e+00 5.83e-01 9.56e+00 angle pdb=" N GLY A 353 " pdb=" CA GLY A 353 " pdb=" C GLY A 353 " ideal model delta sigma weight residual 115.32 111.29 4.03 1.31e+00 5.83e-01 9.45e+00 angle pdb=" N GLY E 353 " pdb=" CA GLY E 353 " pdb=" C GLY E 353 " ideal model delta sigma weight residual 115.32 111.33 3.99 1.31e+00 5.83e-01 9.30e+00 angle pdb=" N GLY D 353 " pdb=" CA GLY D 353 " pdb=" C GLY D 353 " ideal model delta sigma weight residual 115.32 111.33 3.99 1.31e+00 5.83e-01 9.27e+00 ... (remaining 17550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6794 17.97 - 35.95: 823 35.95 - 53.92: 218 53.92 - 71.89: 50 71.89 - 89.87: 15 Dihedral angle restraints: 7900 sinusoidal: 3270 harmonic: 4630 Sorted by residual: dihedral pdb=" CB GLU E 110 " pdb=" CG GLU E 110 " pdb=" CD GLU E 110 " pdb=" OE1 GLU E 110 " ideal model delta sinusoidal sigma weight residual 0.00 89.87 -89.87 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 110 " pdb=" CG GLU A 110 " pdb=" CD GLU A 110 " pdb=" OE1 GLU A 110 " ideal model delta sinusoidal sigma weight residual 0.00 89.85 -89.85 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU C 110 " pdb=" CG GLU C 110 " pdb=" CD GLU C 110 " pdb=" OE1 GLU C 110 " ideal model delta sinusoidal sigma weight residual 0.00 89.84 -89.84 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1234 0.026 - 0.051: 495 0.051 - 0.077: 204 0.077 - 0.102: 51 0.102 - 0.128: 36 Chirality restraints: 2020 Sorted by residual: chirality pdb=" CA ILE B 126 " pdb=" N ILE B 126 " pdb=" C ILE B 126 " pdb=" CB ILE B 126 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE E 126 " pdb=" N ILE E 126 " pdb=" C ILE E 126 " pdb=" CB ILE E 126 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE D 126 " pdb=" N ILE D 126 " pdb=" C ILE D 126 " pdb=" CB ILE D 126 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 2017 not shown) Planarity restraints: 2230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 145 " -0.064 5.00e-02 4.00e+02 9.61e-02 1.48e+01 pdb=" N PRO C 146 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO C 146 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 146 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 145 " 0.064 5.00e-02 4.00e+02 9.60e-02 1.47e+01 pdb=" N PRO E 146 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO E 146 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO E 146 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 145 " 0.064 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A 146 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.052 5.00e-02 4.00e+02 ... (remaining 2227 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 241 2.68 - 3.23: 11958 3.23 - 3.79: 20225 3.79 - 4.34: 29920 4.34 - 4.90: 48448 Nonbonded interactions: 110792 Sorted by model distance: nonbonded pdb="MG MG E 500 " pdb=" O HOH D 646 " model vdw 2.121 2.170 nonbonded pdb="MG MG A 502 " pdb=" O HOH E 645 " model vdw 2.121 2.170 nonbonded pdb="MG MG D 500 " pdb=" O HOH C 646 " model vdw 2.122 2.170 nonbonded pdb="MG MG C 501 " pdb=" O HOH B 646 " model vdw 2.122 2.170 nonbonded pdb="MG MG B 500 " pdb=" O HOH A 646 " model vdw 2.122 2.170 ... (remaining 110787 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 'A' and (resid 84 through 400 or resid 501 through 502)) selection = chain 'B' selection = (chain 'C' and (resid 84 through 400 or resid 501 through 502)) selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 29.770 Find NCS groups from input model: 0.580 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:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.003 0.039 13000 Z= 0.141 Angle : 0.482 6.696 17555 Z= 0.262 Chirality : 0.035 0.128 2020 Planarity : 0.005 0.096 2230 Dihedral : 16.924 89.866 4880 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.14 % Allowed : 23.56 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1575 helix: 0.68 (0.15), residues: 1000 sheet: 1.99 (0.42), residues: 145 loop : -0.91 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 196 HIS 0.003 0.001 HIS E 331 PHE 0.006 0.001 PHE B 352 TYR 0.008 0.001 TYR D 299 ARG 0.001 0.000 ARG C 228 Details of bonding type rmsd hydrogen bonds : bond 0.18889 ( 900) hydrogen bonds : angle 6.33769 ( 2640) covalent geometry : bond 0.00313 (13000) covalent geometry : angle 0.48215 (17555) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 1.461 Fit side-chains REVERT: C 203 LYS cc_start: 0.8819 (mttt) cc_final: 0.8614 (mttt) REVERT: C 270 VAL cc_start: 0.7502 (t) cc_final: 0.6930 (m) REVERT: E 170 GLN cc_start: 0.8549 (mt0) cc_final: 0.8324 (mt0) REVERT: E 368 GLU cc_start: 0.6069 (OUTLIER) cc_final: 0.5699 (mp0) REVERT: E 390 ARG cc_start: 0.7275 (mmt180) cc_final: 0.7022 (mmt180) outliers start: 30 outliers final: 19 residues processed: 199 average time/residue: 1.2598 time to fit residues: 273.5789 Evaluate side-chains 181 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 368 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 40 optimal weight: 30.0000 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 chunk 140 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 HIS ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 HIS ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN D 122 HIS ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 GLN E 122 HIS ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.192594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.127941 restraints weight = 11947.689| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.68 r_work: 0.3018 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13000 Z= 0.156 Angle : 0.508 8.901 17555 Z= 0.267 Chirality : 0.038 0.129 2020 Planarity : 0.005 0.064 2230 Dihedral : 5.109 33.728 1740 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.27 % Allowed : 21.57 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.22), residues: 1575 helix: 2.10 (0.16), residues: 1035 sheet: 2.11 (0.41), residues: 145 loop : -0.58 (0.34), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 196 HIS 0.005 0.001 HIS B 331 PHE 0.020 0.002 PHE E 186 TYR 0.012 0.002 TYR C 299 ARG 0.004 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.05802 ( 900) hydrogen bonds : angle 3.82304 ( 2640) covalent geometry : bond 0.00358 (13000) covalent geometry : angle 0.50784 (17555) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 1.524 Fit side-chains REVERT: A 270 VAL cc_start: 0.7085 (OUTLIER) cc_final: 0.6490 (m) REVERT: A 337 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8151 (ttp-110) REVERT: B 270 VAL cc_start: 0.7160 (OUTLIER) cc_final: 0.6631 (m) REVERT: B 337 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7987 (ttp-110) REVERT: C 124 MET cc_start: 0.9163 (tpt) cc_final: 0.8915 (tpt) REVERT: C 203 LYS cc_start: 0.8681 (mttt) cc_final: 0.8471 (mttt) REVERT: C 270 VAL cc_start: 0.7113 (OUTLIER) cc_final: 0.6813 (t) REVERT: C 337 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7997 (ttp-110) REVERT: E 124 MET cc_start: 0.9164 (tpt) cc_final: 0.8843 (tpt) REVERT: E 270 VAL cc_start: 0.7055 (OUTLIER) cc_final: 0.6489 (m) REVERT: E 337 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7984 (ttp-110) outliers start: 46 outliers final: 12 residues processed: 213 average time/residue: 1.2603 time to fit residues: 292.4953 Evaluate side-chains 190 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 363 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 104 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 327 ASN B 327 ASN E 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.188467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120799 restraints weight = 11928.181| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.79 r_work: 0.2936 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.056 13000 Z= 0.355 Angle : 0.707 10.521 17555 Z= 0.359 Chirality : 0.048 0.139 2020 Planarity : 0.006 0.071 2230 Dihedral : 4.639 37.548 1710 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.70 % Allowed : 21.57 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.21), residues: 1575 helix: 1.70 (0.16), residues: 1035 sheet: 1.67 (0.43), residues: 135 loop : -0.55 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 196 HIS 0.010 0.002 HIS B 331 PHE 0.025 0.003 PHE E 359 TYR 0.022 0.003 TYR D 299 ARG 0.009 0.001 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.07275 ( 900) hydrogen bonds : angle 3.90169 ( 2640) covalent geometry : bond 0.00879 (13000) covalent geometry : angle 0.70710 (17555) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 180 time to evaluate : 1.450 Fit side-chains REVERT: A 210 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7925 (mt) REVERT: A 270 VAL cc_start: 0.7331 (t) cc_final: 0.6739 (m) REVERT: B 194 GLN cc_start: 0.8446 (tp40) cc_final: 0.8195 (tp40) REVERT: B 265 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7298 (tt) REVERT: B 270 VAL cc_start: 0.7558 (OUTLIER) cc_final: 0.6953 (m) REVERT: C 265 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7501 (tt) REVERT: C 268 LEU cc_start: 0.8447 (mt) cc_final: 0.8214 (mp) REVERT: C 270 VAL cc_start: 0.7417 (OUTLIER) cc_final: 0.6780 (m) REVERT: C 329 ASP cc_start: 0.8483 (m-30) cc_final: 0.8275 (m-30) REVERT: D 210 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7910 (mt) REVERT: D 329 ASP cc_start: 0.8622 (m-30) cc_final: 0.8388 (m-30) REVERT: E 124 MET cc_start: 0.9203 (tpt) cc_final: 0.8860 (tpt) REVERT: E 270 VAL cc_start: 0.7319 (t) cc_final: 0.6755 (m) REVERT: E 337 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8066 (ttp-110) outliers start: 66 outliers final: 27 residues processed: 229 average time/residue: 1.1184 time to fit residues: 281.3049 Evaluate side-chains 206 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 363 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 GLN E 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.193338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.125768 restraints weight = 11795.933| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.82 r_work: 0.3033 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13000 Z= 0.141 Angle : 0.503 9.371 17555 Z= 0.260 Chirality : 0.038 0.132 2020 Planarity : 0.004 0.046 2230 Dihedral : 4.102 28.641 1710 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.77 % Allowed : 22.49 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.22), residues: 1575 helix: 2.21 (0.16), residues: 1040 sheet: 1.84 (0.41), residues: 145 loop : -0.56 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 196 HIS 0.004 0.001 HIS B 331 PHE 0.024 0.001 PHE E 186 TYR 0.012 0.002 TYR D 299 ARG 0.003 0.000 ARG D 136 Details of bonding type rmsd hydrogen bonds : bond 0.05252 ( 900) hydrogen bonds : angle 3.57136 ( 2640) covalent geometry : bond 0.00324 (13000) covalent geometry : angle 0.50335 (17555) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 178 time to evaluate : 1.617 Fit side-chains REVERT: A 268 LEU cc_start: 0.8397 (mt) cc_final: 0.8137 (mp) REVERT: A 270 VAL cc_start: 0.7067 (t) cc_final: 0.6473 (m) REVERT: B 270 VAL cc_start: 0.7342 (t) cc_final: 0.6784 (m) REVERT: B 314 ARG cc_start: 0.8616 (ttm-80) cc_final: 0.8402 (ttm170) REVERT: C 314 ARG cc_start: 0.8573 (ttm-80) cc_final: 0.8260 (mmt-90) REVERT: C 387 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7148 (mt) REVERT: D 314 ARG cc_start: 0.8576 (ttm-80) cc_final: 0.8345 (ttm170) REVERT: E 268 LEU cc_start: 0.8358 (mt) cc_final: 0.8129 (mp) REVERT: E 270 VAL cc_start: 0.7180 (t) cc_final: 0.6610 (m) REVERT: E 337 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8085 (ttp-110) outliers start: 53 outliers final: 18 residues processed: 219 average time/residue: 1.1674 time to fit residues: 279.9328 Evaluate side-chains 192 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 363 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN C 298 ASN D 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.189956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.119983 restraints weight = 11853.536| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.81 r_work: 0.2978 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 13000 Z= 0.268 Angle : 0.628 10.235 17555 Z= 0.318 Chirality : 0.044 0.133 2020 Planarity : 0.005 0.054 2230 Dihedral : 4.451 34.171 1710 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.99 % Allowed : 21.99 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.22), residues: 1575 helix: 1.96 (0.16), residues: 1035 sheet: 1.80 (0.42), residues: 145 loop : -0.54 (0.34), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 196 HIS 0.008 0.002 HIS B 331 PHE 0.020 0.002 PHE B 359 TYR 0.021 0.003 TYR D 299 ARG 0.007 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.06382 ( 900) hydrogen bonds : angle 3.70967 ( 2640) covalent geometry : bond 0.00663 (13000) covalent geometry : angle 0.62810 (17555) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 167 time to evaluate : 1.497 Fit side-chains REVERT: A 268 LEU cc_start: 0.8388 (mt) cc_final: 0.8133 (mp) REVERT: A 270 VAL cc_start: 0.7212 (t) cc_final: 0.6623 (m) REVERT: A 338 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8573 (tt) REVERT: B 270 VAL cc_start: 0.7459 (t) cc_final: 0.6845 (m) REVERT: C 160 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6287 (mt-10) REVERT: C 265 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7293 (tt) REVERT: C 270 VAL cc_start: 0.7292 (t) cc_final: 0.6707 (m) REVERT: C 387 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7108 (mt) REVERT: E 270 VAL cc_start: 0.7233 (t) cc_final: 0.6690 (m) REVERT: E 337 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8131 (ttp-110) outliers start: 56 outliers final: 30 residues processed: 209 average time/residue: 1.0895 time to fit residues: 251.2167 Evaluate side-chains 201 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 213 GLU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 363 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 103 optimal weight: 0.6980 chunk 69 optimal weight: 0.1980 chunk 121 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 146 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 120 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 236 GLN B 298 ASN C 236 GLN C 298 ASN D 236 GLN E 194 GLN E 236 GLN E 298 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.195476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.137122 restraints weight = 12029.818| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.65 r_work: 0.3085 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13000 Z= 0.113 Angle : 0.472 9.198 17555 Z= 0.243 Chirality : 0.037 0.131 2020 Planarity : 0.003 0.042 2230 Dihedral : 3.904 26.056 1710 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.35 % Allowed : 23.91 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.22), residues: 1575 helix: 2.43 (0.16), residues: 1040 sheet: 1.76 (0.41), residues: 145 loop : -0.54 (0.35), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 196 HIS 0.003 0.001 HIS D 331 PHE 0.026 0.001 PHE E 186 TYR 0.008 0.001 TYR C 299 ARG 0.003 0.000 ARG D 136 Details of bonding type rmsd hydrogen bonds : bond 0.04602 ( 900) hydrogen bonds : angle 3.44117 ( 2640) covalent geometry : bond 0.00238 (13000) covalent geometry : angle 0.47226 (17555) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 1.506 Fit side-chains REVERT: A 268 LEU cc_start: 0.8399 (mt) cc_final: 0.8152 (mp) REVERT: A 270 VAL cc_start: 0.7368 (t) cc_final: 0.6783 (m) REVERT: B 270 VAL cc_start: 0.7425 (t) cc_final: 0.7028 (m) REVERT: B 314 ARG cc_start: 0.8379 (ttm-80) cc_final: 0.8121 (mmt-90) REVERT: C 270 VAL cc_start: 0.7432 (t) cc_final: 0.7138 (t) REVERT: C 314 ARG cc_start: 0.8299 (ttm-80) cc_final: 0.8041 (mmt-90) REVERT: C 387 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7377 (mt) REVERT: D 314 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.8072 (mmt-90) REVERT: E 124 MET cc_start: 0.9244 (tpt) cc_final: 0.8729 (tpt) REVERT: E 268 LEU cc_start: 0.8430 (mt) cc_final: 0.8205 (mp) REVERT: E 270 VAL cc_start: 0.7312 (t) cc_final: 0.6808 (m) REVERT: E 337 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7901 (ttp-110) outliers start: 33 outliers final: 8 residues processed: 204 average time/residue: 1.1328 time to fit residues: 253.9474 Evaluate side-chains 179 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 337 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 92 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 132 optimal weight: 0.1980 chunk 152 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 69 optimal weight: 0.0980 chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 0.0470 chunk 105 optimal weight: 0.8980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN B 298 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.196442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.136116 restraints weight = 11951.511| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.66 r_work: 0.3048 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13000 Z= 0.109 Angle : 0.461 8.655 17555 Z= 0.239 Chirality : 0.037 0.132 2020 Planarity : 0.003 0.041 2230 Dihedral : 3.488 13.836 1705 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.63 % Allowed : 23.63 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.22), residues: 1575 helix: 2.84 (0.16), residues: 1005 sheet: 1.79 (0.40), residues: 145 loop : -0.82 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 196 HIS 0.003 0.001 HIS B 331 PHE 0.019 0.001 PHE A 186 TYR 0.009 0.001 TYR E 299 ARG 0.002 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 900) hydrogen bonds : angle 3.33491 ( 2640) covalent geometry : bond 0.00235 (13000) covalent geometry : angle 0.46092 (17555) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 1.387 Fit side-chains REVERT: A 268 LEU cc_start: 0.8256 (mt) cc_final: 0.8015 (mp) REVERT: A 368 GLU cc_start: 0.5745 (OUTLIER) cc_final: 0.5269 (mp0) REVERT: B 314 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.8112 (mmt-90) REVERT: C 206 ILE cc_start: 0.8565 (mt) cc_final: 0.8358 (mp) REVERT: C 270 VAL cc_start: 0.7174 (t) cc_final: 0.6870 (t) REVERT: C 314 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.8068 (mmt-90) REVERT: C 387 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7221 (mt) REVERT: D 314 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.8045 (mmt-90) REVERT: E 337 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7990 (ttp-110) outliers start: 37 outliers final: 14 residues processed: 203 average time/residue: 1.0769 time to fit residues: 240.8443 Evaluate side-chains 179 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 400 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 31 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 327 ASN B 298 ASN B 327 ASN D 121 GLN E 298 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.189617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.127853 restraints weight = 11953.159| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.60 r_work: 0.2967 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13000 Z= 0.254 Angle : 0.610 9.882 17555 Z= 0.310 Chirality : 0.043 0.135 2020 Planarity : 0.005 0.048 2230 Dihedral : 3.923 14.269 1705 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.78 % Allowed : 24.13 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.21), residues: 1575 helix: 2.31 (0.16), residues: 1005 sheet: 1.84 (0.42), residues: 145 loop : -0.86 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 375 HIS 0.008 0.002 HIS B 331 PHE 0.019 0.002 PHE E 186 TYR 0.020 0.003 TYR E 299 ARG 0.007 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.06094 ( 900) hydrogen bonds : angle 3.61076 ( 2640) covalent geometry : bond 0.00626 (13000) covalent geometry : angle 0.61028 (17555) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 1.419 Fit side-chains REVERT: A 210 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7888 (mt) REVERT: A 268 LEU cc_start: 0.8388 (mt) cc_final: 0.8157 (mp) REVERT: B 270 VAL cc_start: 0.7550 (t) cc_final: 0.6946 (m) REVERT: C 270 VAL cc_start: 0.7401 (t) cc_final: 0.6818 (m) REVERT: C 314 ARG cc_start: 0.8471 (ttm-80) cc_final: 0.8218 (ttm170) REVERT: C 387 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7322 (mt) REVERT: D 210 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7872 (mt) REVERT: D 314 ARG cc_start: 0.8426 (ttm-80) cc_final: 0.8189 (ttm170) REVERT: E 186 PHE cc_start: 0.7818 (t80) cc_final: 0.7605 (t80) REVERT: E 270 VAL cc_start: 0.7300 (t) cc_final: 0.6752 (m) REVERT: E 337 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8012 (ttp-110) outliers start: 39 outliers final: 22 residues processed: 190 average time/residue: 1.1542 time to fit residues: 240.7391 Evaluate side-chains 195 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 400 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 89 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 298 ASN D 121 GLN E 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.194989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.136627 restraints weight = 11836.822| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.48 r_work: 0.3055 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13000 Z= 0.123 Angle : 0.496 8.856 17555 Z= 0.255 Chirality : 0.037 0.132 2020 Planarity : 0.003 0.040 2230 Dihedral : 3.621 13.504 1705 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.85 % Allowed : 25.12 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.22), residues: 1575 helix: 2.47 (0.16), residues: 1040 sheet: 1.84 (0.42), residues: 145 loop : -0.51 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 196 HIS 0.003 0.001 HIS D 331 PHE 0.022 0.001 PHE E 186 TYR 0.010 0.001 TYR E 299 ARG 0.002 0.000 ARG D 136 Details of bonding type rmsd hydrogen bonds : bond 0.04681 ( 900) hydrogen bonds : angle 3.42239 ( 2640) covalent geometry : bond 0.00274 (13000) covalent geometry : angle 0.49618 (17555) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 1.482 Fit side-chains REVERT: A 268 LEU cc_start: 0.8453 (mt) cc_final: 0.8218 (mp) REVERT: A 270 VAL cc_start: 0.7242 (t) cc_final: 0.6635 (m) REVERT: A 338 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8560 (tt) REVERT: B 270 VAL cc_start: 0.7554 (t) cc_final: 0.7008 (m) REVERT: B 314 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.8169 (ttm170) REVERT: C 270 VAL cc_start: 0.7488 (t) cc_final: 0.6912 (m) REVERT: C 314 ARG cc_start: 0.8322 (ttm-80) cc_final: 0.8063 (mmt-90) REVERT: C 387 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7375 (mt) REVERT: D 210 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7932 (mt) REVERT: D 314 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.8119 (ttm170) REVERT: E 270 VAL cc_start: 0.7336 (t) cc_final: 0.6792 (m) REVERT: E 337 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7946 (ttp-110) outliers start: 26 outliers final: 15 residues processed: 189 average time/residue: 1.1640 time to fit residues: 241.4920 Evaluate side-chains 184 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 47 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 102 optimal weight: 0.0000 chunk 131 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN B 298 ASN C 298 ASN E 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.194432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.129208 restraints weight = 11881.579| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.74 r_work: 0.3023 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13000 Z= 0.131 Angle : 0.503 8.994 17555 Z= 0.259 Chirality : 0.038 0.132 2020 Planarity : 0.004 0.040 2230 Dihedral : 3.603 13.669 1705 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.64 % Allowed : 25.48 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.22), residues: 1575 helix: 2.70 (0.16), residues: 1005 sheet: 1.87 (0.41), residues: 145 loop : -0.81 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 196 HIS 0.004 0.001 HIS B 331 PHE 0.021 0.001 PHE A 186 TYR 0.012 0.002 TYR D 299 ARG 0.003 0.000 ARG C 332 Details of bonding type rmsd hydrogen bonds : bond 0.04789 ( 900) hydrogen bonds : angle 3.40978 ( 2640) covalent geometry : bond 0.00299 (13000) covalent geometry : angle 0.50337 (17555) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.773 Fit side-chains REVERT: A 268 LEU cc_start: 0.8328 (mt) cc_final: 0.8090 (mp) REVERT: A 338 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8520 (tt) REVERT: B 270 VAL cc_start: 0.7352 (t) cc_final: 0.6815 (m) REVERT: B 314 ARG cc_start: 0.8377 (ttm-80) cc_final: 0.8156 (mmt-90) REVERT: C 270 VAL cc_start: 0.7277 (t) cc_final: 0.6994 (t) REVERT: C 314 ARG cc_start: 0.8349 (ttm-80) cc_final: 0.8051 (mmt-90) REVERT: C 387 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7272 (mt) REVERT: D 210 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7864 (mt) REVERT: D 314 ARG cc_start: 0.8354 (ttm-80) cc_final: 0.8114 (ttm170) REVERT: E 337 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7926 (ttp-110) outliers start: 23 outliers final: 17 residues processed: 182 average time/residue: 1.2172 time to fit residues: 242.1816 Evaluate side-chains 184 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN B 298 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.191054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.123946 restraints weight = 11914.847| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.74 r_work: 0.2997 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 13000 Z= 0.230 Angle : 0.605 9.812 17555 Z= 0.308 Chirality : 0.042 0.135 2020 Planarity : 0.004 0.046 2230 Dihedral : 3.908 14.029 1705 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.35 % Allowed : 25.12 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.21), residues: 1575 helix: 2.32 (0.16), residues: 1005 sheet: 1.87 (0.42), residues: 145 loop : -0.84 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 196 HIS 0.007 0.002 HIS B 331 PHE 0.020 0.002 PHE B 359 TYR 0.019 0.002 TYR D 299 ARG 0.005 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.05917 ( 900) hydrogen bonds : angle 3.58753 ( 2640) covalent geometry : bond 0.00564 (13000) covalent geometry : angle 0.60487 (17555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9707.12 seconds wall clock time: 167 minutes 29.54 seconds (10049.54 seconds total)