Starting phenix.real_space_refine on Thu Jul 31 01:49:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tul_41624/07_2025/8tul_41624.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tul_41624/07_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_41624/07_2025/8tul_41624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tul_41624/07_2025/8tul_41624.map" model { file = "/net/cci-nas-00/data/ceres_data/8tul_41624/07_2025/8tul_41624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tul_41624/07_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.56, 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: 3.05 Conformation dependent library (CDL) restraints added in 1.7 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: 1.28 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: 3.59 Time building geometry restraints manager: 3.63 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 29.440 Find NCS groups from input model: 0.610 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:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.860 ------------------------------------------------------------------------------- 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 : 1.318 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: 1.2683 time to fit residues: 275.1433 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 : 1.256 ------------------------------------------------------------------------------- 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: 0.3017 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- 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 : 1.356 Fit side-chains REVERT: A 270 VAL cc_start: 0.7053 (OUTLIER) cc_final: 0.6463 (m) REVERT: A 337 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8146 (ttp-110) REVERT: B 270 VAL cc_start: 0.7130 (OUTLIER) cc_final: 0.6604 (m) REVERT: B 337 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7982 (ttp-110) REVERT: C 124 MET cc_start: 0.9162 (tpt) cc_final: 0.8912 (tpt) REVERT: C 203 LYS cc_start: 0.8681 (mttt) cc_final: 0.8470 (mttt) REVERT: C 270 VAL cc_start: 0.7088 (OUTLIER) cc_final: 0.6789 (t) REVERT: C 337 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7993 (ttp-110) REVERT: E 124 MET cc_start: 0.9164 (tpt) cc_final: 0.8842 (tpt) REVERT: E 270 VAL cc_start: 0.7027 (OUTLIER) cc_final: 0.6466 (m) REVERT: E 337 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7977 (ttp-110) outliers start: 46 outliers final: 12 residues processed: 213 average time/residue: 1.2689 time to fit residues: 294.3664 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 : 1.354 ------------------------------------------------------------------------------- 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: 1.9990 chunk 102 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.189571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.122203 restraints weight = 11928.394| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.81 r_work: 0.2941 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 13000 Z= 0.296 Angle : 0.640 9.692 17555 Z= 0.327 Chirality : 0.045 0.133 2020 Planarity : 0.005 0.059 2230 Dihedral : 4.429 34.935 1710 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.56 % Allowed : 21.57 % Favored : 73.88 % 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: 2.09 (0.22), residues: 1575 helix: 1.96 (0.16), residues: 1030 sheet: 1.96 (0.41), residues: 145 loop : -0.33 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 196 HIS 0.009 0.002 HIS B 331 PHE 0.022 0.002 PHE E 359 TYR 0.019 0.003 TYR D 299 ARG 0.008 0.001 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.06759 ( 900) hydrogen bonds : angle 3.81666 ( 2640) covalent geometry : bond 0.00734 (13000) covalent geometry : angle 0.63992 (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 242 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 178 time to evaluate : 1.454 Fit side-chains REVERT: A 210 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7893 (mt) REVERT: A 270 VAL cc_start: 0.7074 (t) cc_final: 0.6489 (m) REVERT: A 337 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8173 (ttp-110) REVERT: B 194 GLN cc_start: 0.8416 (tp40) cc_final: 0.8164 (tp40) REVERT: B 270 VAL cc_start: 0.7342 (OUTLIER) cc_final: 0.6757 (m) REVERT: B 337 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8058 (ttp-110) REVERT: C 265 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7460 (tt) REVERT: C 329 ASP cc_start: 0.8466 (m-30) cc_final: 0.8205 (m-30) REVERT: D 329 ASP cc_start: 0.8613 (m-30) cc_final: 0.8349 (m-30) REVERT: E 124 MET cc_start: 0.9189 (tpt) cc_final: 0.8837 (tpt) REVERT: E 270 VAL cc_start: 0.7208 (t) cc_final: 0.6661 (m) REVERT: E 337 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8024 (ttp-110) outliers start: 64 outliers final: 32 residues processed: 225 average time/residue: 1.1583 time to fit residues: 285.7179 Evaluate side-chains 205 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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 337 ARG Chi-restraints excluded: chain A residue 338 LEU 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 337 ARG 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 232 HIS Chi-restraints excluded: chain C residue 265 LEU 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 213 GLU 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 342 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: 2.9990 chunk 131 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 143 optimal weight: 30.0000 chunk 95 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 GLN B 298 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.193865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.130009 restraints weight = 11812.334| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.71 r_work: 0.3036 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1561 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= 0.135 Angle : 0.488 9.045 17555 Z= 0.253 Chirality : 0.038 0.131 2020 Planarity : 0.004 0.049 2230 Dihedral : 4.007 28.154 1710 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.13 % Allowed : 21.71 % Favored : 74.16 % 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: 2.48 (0.22), residues: 1575 helix: 2.35 (0.16), residues: 1035 sheet: 1.83 (0.40), residues: 145 loop : -0.38 (0.35), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 196 HIS 0.004 0.001 HIS D 331 PHE 0.023 0.001 PHE E 186 TYR 0.011 0.001 TYR D 299 ARG 0.003 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.05128 ( 900) hydrogen bonds : angle 3.54723 ( 2640) covalent geometry : bond 0.00308 (13000) covalent geometry : angle 0.48793 (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 237 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 179 time to evaluate : 1.370 Fit side-chains REVERT: A 270 VAL cc_start: 0.7078 (OUTLIER) cc_final: 0.6542 (m) REVERT: A 337 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8161 (ttp-110) REVERT: B 314 ARG cc_start: 0.8393 (ttm-80) cc_final: 0.8159 (ttm170) REVERT: B 337 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.8007 (ttp-110) REVERT: C 268 LEU cc_start: 0.8409 (mt) cc_final: 0.8186 (mp) REVERT: C 270 VAL cc_start: 0.7240 (t) cc_final: 0.6952 (t) REVERT: C 314 ARG cc_start: 0.8356 (ttm-80) cc_final: 0.8063 (mmt-90) REVERT: C 387 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7291 (mt) REVERT: D 210 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7856 (mt) REVERT: D 314 ARG cc_start: 0.8371 (ttm-80) cc_final: 0.8099 (ttm170) REVERT: E 124 MET cc_start: 0.9231 (tpt) cc_final: 0.8889 (tpt) REVERT: E 270 VAL cc_start: 0.7220 (OUTLIER) cc_final: 0.6671 (m) REVERT: E 337 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7953 (ttp-110) outliers start: 58 outliers final: 21 residues processed: 222 average time/residue: 1.2135 time to fit residues: 294.4734 Evaluate side-chains 200 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 2.234 ------------------------------------------------------------------------------- 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 A residue 338 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 400 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 338 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 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 213 GLU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 120 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN B 327 ASN C 298 ASN C 327 ASN D 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.190418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120525 restraints weight = 11862.147| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.80 r_work: 0.2984 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13000 Z= 0.250 Angle : 0.601 10.004 17555 Z= 0.306 Chirality : 0.043 0.134 2020 Planarity : 0.005 0.050 2230 Dihedral : 4.371 33.608 1710 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.63 % Allowed : 22.14 % Favored : 74.23 % 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: 2.16 (0.22), residues: 1575 helix: 2.09 (0.16), residues: 1035 sheet: 1.81 (0.41), residues: 145 loop : -0.49 (0.34), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 196 HIS 0.008 0.002 HIS B 331 PHE 0.018 0.002 PHE B 359 TYR 0.021 0.003 TYR D 299 ARG 0.005 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.06207 ( 900) hydrogen bonds : angle 3.67291 ( 2640) covalent geometry : bond 0.00615 (13000) covalent geometry : angle 0.60118 (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 224 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 2.180 Fit side-chains REVERT: A 268 LEU cc_start: 0.8404 (mt) cc_final: 0.8171 (mp) REVERT: A 337 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8263 (ttp-110) REVERT: B 270 VAL cc_start: 0.7334 (t) cc_final: 0.6798 (m) REVERT: B 337 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8129 (ttp-110) REVERT: C 265 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7322 (tt) REVERT: C 314 ARG cc_start: 0.8625 (ttm-80) cc_final: 0.8406 (ttm170) REVERT: C 387 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7073 (mt) REVERT: D 210 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7798 (mt) REVERT: D 329 ASP cc_start: 0.8788 (m-30) cc_final: 0.8502 (m-30) REVERT: E 270 VAL cc_start: 0.7120 (t) cc_final: 0.6557 (m) REVERT: E 337 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8144 (ttp-110) outliers start: 51 outliers final: 30 residues processed: 211 average time/residue: 1.3281 time to fit residues: 307.0872 Evaluate side-chains 205 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 355 MET 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 337 ARG 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 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 210 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 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: 0.5980 chunk 69 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 120 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 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 236 GLN B 236 GLN B 298 ASN C 236 GLN C 298 ASN D 236 GLN E 298 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.194365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.133775 restraints weight = 12018.710| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.68 r_work: 0.3040 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13000 Z= 0.127 Angle : 0.487 9.183 17555 Z= 0.251 Chirality : 0.037 0.131 2020 Planarity : 0.004 0.042 2230 Dihedral : 3.979 27.700 1710 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.56 % Allowed : 22.63 % Favored : 73.81 % 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: 2.49 (0.22), residues: 1575 helix: 2.41 (0.16), residues: 1040 sheet: 1.78 (0.41), residues: 145 loop : -0.53 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 196 HIS 0.004 0.001 HIS D 331 PHE 0.021 0.001 PHE E 186 TYR 0.012 0.001 TYR D 299 ARG 0.002 0.000 ARG D 136 Details of bonding type rmsd hydrogen bonds : bond 0.04922 ( 900) hydrogen bonds : angle 3.47418 ( 2640) covalent geometry : bond 0.00285 (13000) covalent geometry : angle 0.48746 (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 227 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 1.431 Fit side-chains REVERT: A 268 LEU cc_start: 0.8462 (mt) cc_final: 0.8239 (mp) REVERT: A 305 ASP cc_start: 0.8369 (m-30) cc_final: 0.8166 (m-30) REVERT: A 337 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8177 (ttp-110) REVERT: A 338 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8468 (tt) REVERT: B 270 VAL cc_start: 0.7436 (t) cc_final: 0.6942 (m) REVERT: B 314 ARG cc_start: 0.8413 (ttm-80) cc_final: 0.8181 (ttm170) REVERT: B 337 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8037 (ttp-110) REVERT: C 270 VAL cc_start: 0.7328 (t) cc_final: 0.7085 (t) REVERT: C 314 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.8066 (mmt-90) REVERT: C 344 MET cc_start: 0.8843 (mtt) cc_final: 0.8592 (mtp) REVERT: C 387 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7353 (mt) REVERT: D 210 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7874 (mt) REVERT: D 314 ARG cc_start: 0.8355 (ttm-80) cc_final: 0.8104 (ttm170) REVERT: E 124 MET cc_start: 0.9239 (tpt) cc_final: 0.8694 (tpt) REVERT: E 186 PHE cc_start: 0.7842 (t80) cc_final: 0.7628 (t80) REVERT: E 270 VAL cc_start: 0.7304 (t) cc_final: 0.6785 (m) REVERT: E 337 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7948 (ttp-110) outliers start: 50 outliers final: 21 residues processed: 215 average time/residue: 1.1846 time to fit residues: 279.1079 Evaluate side-chains 201 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 1.383 ------------------------------------------------------------------------------- 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 337 ARG 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 232 HIS Chi-restraints excluded: chain B residue 337 ARG 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 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL 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 363 LEU Chi-restraints excluded: chain E residue 400 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 92 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 118 optimal weight: 0.5980 chunk 132 optimal weight: 0.3980 chunk 152 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 D 298 ASN E 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.193740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131852 restraints weight = 11912.247| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.66 r_work: 0.3025 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13000 Z= 0.143 Angle : 0.501 9.281 17555 Z= 0.258 Chirality : 0.038 0.133 2020 Planarity : 0.004 0.042 2230 Dihedral : 3.998 29.379 1710 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.42 % Allowed : 22.56 % 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: 2.52 (0.22), residues: 1575 helix: 2.43 (0.16), residues: 1040 sheet: 1.80 (0.41), residues: 145 loop : -0.55 (0.34), residues: 390 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 0.018 0.002 PHE E 186 TYR 0.014 0.002 TYR D 299 ARG 0.003 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.05062 ( 900) hydrogen bonds : angle 3.47100 ( 2640) covalent geometry : bond 0.00333 (13000) covalent geometry : angle 0.50069 (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 221 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 173 time to evaluate : 1.494 Fit side-chains REVERT: A 268 LEU cc_start: 0.8416 (mt) cc_final: 0.8183 (mp) REVERT: A 337 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8187 (ttp-110) REVERT: B 270 VAL cc_start: 0.7455 (t) cc_final: 0.6924 (m) REVERT: B 314 ARG cc_start: 0.8423 (ttm-80) cc_final: 0.8191 (ttm170) REVERT: B 337 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7998 (ttp-110) REVERT: C 270 VAL cc_start: 0.7378 (t) cc_final: 0.6848 (m) REVERT: C 314 ARG cc_start: 0.8404 (ttm-80) cc_final: 0.8097 (mmt-90) REVERT: C 387 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7385 (mt) REVERT: D 210 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7911 (mt) REVERT: D 314 ARG cc_start: 0.8384 (ttm-80) cc_final: 0.8134 (ttm170) REVERT: E 124 MET cc_start: 0.9250 (tpt) cc_final: 0.8704 (tpt) REVERT: E 186 PHE cc_start: 0.7888 (t80) cc_final: 0.7669 (t80) REVERT: E 270 VAL cc_start: 0.7310 (t) cc_final: 0.6741 (m) REVERT: E 337 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.8108 (ttp-110) outliers start: 48 outliers final: 25 residues processed: 208 average time/residue: 1.4308 time to fit residues: 324.7309 Evaluate side-chains 197 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 337 ARG 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 232 HIS Chi-restraints excluded: chain B residue 337 ARG 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 232 HIS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 232 HIS 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 363 LEU 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: 0.9990 chunk 148 optimal weight: 0.9990 chunk 86 optimal weight: 0.0770 chunk 98 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 298 ASN C 298 ASN D 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 = 0.4092 r_free = 0.4092 target = 0.193852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.131277 restraints weight = 11970.455| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.66 r_work: 0.3024 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13000 Z= 0.143 Angle : 0.504 9.245 17555 Z= 0.259 Chirality : 0.038 0.133 2020 Planarity : 0.004 0.041 2230 Dihedral : 3.975 29.167 1710 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.99 % Allowed : 23.13 % Favored : 73.88 % 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: 2.54 (0.22), residues: 1575 helix: 2.44 (0.16), residues: 1040 sheet: 1.84 (0.41), residues: 145 loop : -0.53 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 196 HIS 0.004 0.001 HIS B 331 PHE 0.021 0.002 PHE A 186 TYR 0.014 0.002 TYR D 299 ARG 0.002 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.05036 ( 900) hydrogen bonds : angle 3.45047 ( 2640) covalent geometry : bond 0.00333 (13000) covalent geometry : angle 0.50403 (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 210 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 1.557 Fit side-chains REVERT: A 268 LEU cc_start: 0.8407 (mt) cc_final: 0.8169 (mp) REVERT: A 337 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8193 (ttp-110) REVERT: B 270 VAL cc_start: 0.7439 (t) cc_final: 0.6909 (m) REVERT: B 314 ARG cc_start: 0.8419 (ttm-80) cc_final: 0.8180 (ttm170) REVERT: B 337 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8014 (ttp-110) REVERT: B 383 MET cc_start: 0.6786 (mmt) cc_final: 0.6364 (mmm) REVERT: C 270 VAL cc_start: 0.7374 (t) cc_final: 0.6816 (m) REVERT: C 314 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8087 (mmt-90) REVERT: C 387 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7338 (mt) REVERT: D 210 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7897 (mt) REVERT: D 270 VAL cc_start: 0.7534 (t) cc_final: 0.7056 (m) REVERT: D 314 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8137 (ttm170) REVERT: E 124 MET cc_start: 0.9236 (tpt) cc_final: 0.8705 (tpt) REVERT: E 270 VAL cc_start: 0.7309 (t) cc_final: 0.6744 (m) REVERT: E 337 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.8082 (ttp-110) outliers start: 42 outliers final: 27 residues processed: 198 average time/residue: 1.4647 time to fit residues: 316.6569 Evaluate side-chains 199 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 355 MET 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 232 HIS Chi-restraints excluded: chain B residue 337 ARG 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 232 HIS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 232 HIS 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 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: 0.3980 chunk 23 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN B 298 ASN C 298 ASN D 298 ASN E 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.195109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.134146 restraints weight = 11806.237| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.65 r_work: 0.3038 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1802 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= 0.125 Angle : 0.484 9.009 17555 Z= 0.249 Chirality : 0.037 0.133 2020 Planarity : 0.003 0.041 2230 Dihedral : 3.867 27.692 1710 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.56 % Allowed : 23.77 % Favored : 73.67 % 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: 2.65 (0.22), residues: 1575 helix: 2.74 (0.16), residues: 1005 sheet: 1.83 (0.40), residues: 145 loop : -0.82 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 196 HIS 0.003 0.001 HIS D 331 PHE 0.015 0.001 PHE B 186 TYR 0.011 0.001 TYR D 299 ARG 0.002 0.000 ARG D 136 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 900) hydrogen bonds : angle 3.38764 ( 2640) covalent geometry : bond 0.00283 (13000) covalent geometry : angle 0.48352 (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 207 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 2.271 Fit side-chains REVERT: A 268 LEU cc_start: 0.8313 (mt) cc_final: 0.8049 (mp) REVERT: A 270 VAL cc_start: 0.7123 (t) cc_final: 0.6767 (t) REVERT: A 337 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8155 (ttp-110) REVERT: B 270 VAL cc_start: 0.7296 (t) cc_final: 0.6764 (m) REVERT: B 314 ARG cc_start: 0.8387 (ttm-80) cc_final: 0.8167 (mmt-90) REVERT: B 337 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8029 (ttp-110) REVERT: B 383 MET cc_start: 0.6713 (mmt) cc_final: 0.6278 (mmm) REVERT: C 270 VAL cc_start: 0.7219 (t) cc_final: 0.6665 (m) REVERT: C 314 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.8054 (mmt-90) REVERT: C 387 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7277 (mt) REVERT: D 210 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7852 (mt) REVERT: D 314 ARG cc_start: 0.8366 (ttm-80) cc_final: 0.8110 (ttm170) REVERT: E 124 MET cc_start: 0.9223 (tpt) cc_final: 0.8667 (tpt) REVERT: E 337 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7932 (ttp-110) outliers start: 36 outliers final: 22 residues processed: 197 average time/residue: 1.7018 time to fit residues: 365.8731 Evaluate side-chains 191 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 1.752 ------------------------------------------------------------------------------- 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 337 ARG Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 355 MET 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 232 HIS Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 338 LEU 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 232 HIS Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 363 LEU 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: 0.0980 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: 9.9990 chunk 131 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 C 298 ASN C 327 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.191926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132156 restraints weight = 11840.672| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.64 r_work: 0.2973 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13000 Z= 0.199 Angle : 0.564 9.652 17555 Z= 0.287 Chirality : 0.040 0.134 2020 Planarity : 0.004 0.040 2230 Dihedral : 4.153 31.880 1710 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.42 % Allowed : 23.99 % Favored : 73.59 % 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: 2.34 (0.21), residues: 1575 helix: 2.44 (0.16), residues: 1005 sheet: 1.86 (0.42), residues: 145 loop : -0.83 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 196 HIS 0.007 0.001 HIS B 331 PHE 0.023 0.002 PHE E 186 TYR 0.017 0.002 TYR D 299 ARG 0.005 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.05643 ( 900) hydrogen bonds : angle 3.53081 ( 2640) covalent geometry : bond 0.00483 (13000) covalent geometry : angle 0.56370 (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 206 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 1.505 Fit side-chains REVERT: A 268 LEU cc_start: 0.8379 (mt) cc_final: 0.8131 (mp) REVERT: A 270 VAL cc_start: 0.7267 (t) cc_final: 0.6685 (m) REVERT: A 337 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8157 (ttp-110) REVERT: B 270 VAL cc_start: 0.7411 (t) cc_final: 0.6856 (m) REVERT: B 314 ARG cc_start: 0.8468 (ttm-80) cc_final: 0.8232 (ttm170) REVERT: B 337 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.8059 (ttp-110) REVERT: C 270 VAL cc_start: 0.7303 (t) cc_final: 0.6733 (m) REVERT: C 314 ARG cc_start: 0.8456 (ttm-80) cc_final: 0.8231 (ttm170) REVERT: C 387 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7310 (mt) REVERT: D 210 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7856 (mt) REVERT: D 270 VAL cc_start: 0.7468 (t) cc_final: 0.6984 (m) REVERT: D 314 ARG cc_start: 0.8437 (ttm-80) cc_final: 0.8183 (ttm170) REVERT: E 124 MET cc_start: 0.9241 (tpt) cc_final: 0.8733 (tpt) REVERT: E 270 VAL cc_start: 0.7308 (t) cc_final: 0.6757 (m) REVERT: E 337 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8038 (ttp-110) outliers start: 34 outliers final: 22 residues processed: 198 average time/residue: 1.3640 time to fit residues: 297.8439 Evaluate side-chains 200 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 337 ARG Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 138 GLU 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 232 HIS Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 GLU 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 232 HIS Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 363 LEU 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: 7.9990 chunk 85 optimal weight: 0.5980 chunk 122 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 9 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN B 298 ASN C 298 ASN D 298 ASN E 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.195970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.134363 restraints weight = 11930.653| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.66 r_work: 0.3012 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1796 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= 0.130 Angle : 0.499 9.062 17555 Z= 0.257 Chirality : 0.038 0.132 2020 Planarity : 0.003 0.042 2230 Dihedral : 3.910 27.679 1710 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.21 % Allowed : 23.99 % Favored : 73.81 % 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: 2.58 (0.21), residues: 1575 helix: 2.67 (0.16), residues: 1005 sheet: 1.84 (0.41), residues: 145 loop : -0.81 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 196 HIS 0.003 0.001 HIS D 331 PHE 0.018 0.001 PHE C 359 TYR 0.012 0.002 TYR D 299 ARG 0.002 0.000 ARG D 136 Details of bonding type rmsd hydrogen bonds : bond 0.04817 ( 900) hydrogen bonds : angle 3.41543 ( 2640) covalent geometry : bond 0.00296 (13000) covalent geometry : angle 0.49911 (17555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10943.93 seconds wall clock time: 192 minutes 48.69 seconds (11568.69 seconds total)