Starting phenix.real_space_refine on Sun Nov 17 05:40:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tul_41624/11_2024/8tul_41624.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tul_41624/11_2024/8tul_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tul_41624/11_2024/8tul_41624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tul_41624/11_2024/8tul_41624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tul_41624/11_2024/8tul_41624.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tul_41624/11_2024/8tul_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-5513/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: 6.82, per 1000 atoms: 0.52 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: 3.01 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: 1.32 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: 3.97 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3259 1.33 - 1.45: 2212 1.45 - 1.57: 7409 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 13000 Sorted by residual: bond pdb=" C MET D 336 " pdb=" O MET D 336 " ideal model delta sigma weight residual 1.236 1.214 0.022 1.29e-02 6.01e+03 3.03e+00 bond pdb=" C MET E 336 " pdb=" O MET E 336 " ideal model delta sigma weight residual 1.236 1.215 0.022 1.29e-02 6.01e+03 2.80e+00 bond pdb=" C MET C 336 " pdb=" O MET C 336 " ideal model delta sigma weight residual 1.236 1.215 0.021 1.29e-02 6.01e+03 2.75e+00 bond pdb=" C MET B 336 " pdb=" O MET B 336 " ideal model delta sigma weight residual 1.236 1.215 0.021 1.29e-02 6.01e+03 2.75e+00 bond pdb=" C MET A 336 " pdb=" O MET A 336 " ideal model delta sigma weight residual 1.236 1.215 0.021 1.29e-02 6.01e+03 2.72e+00 ... (remaining 12995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 17151 1.34 - 2.68: 344 2.68 - 4.02: 32 4.02 - 5.36: 18 5.36 - 6.70: 10 Bond angle restraints: 17555 Sorted by residual: angle pdb=" N GLY C 353 " pdb=" CA GLY C 353 " pdb=" C GLY C 353 " ideal model delta sigma weight residual 115.32 111.27 4.05 1.31e+00 5.83e-01 9.56e+00 angle pdb=" N GLY B 353 " pdb=" CA GLY B 353 " pdb=" C GLY B 353 " ideal model delta sigma weight residual 115.32 111.27 4.05 1.31e+00 5.83e-01 9.56e+00 angle pdb=" N GLY A 353 " pdb=" CA GLY A 353 " pdb=" C GLY A 353 " ideal model delta sigma weight residual 115.32 111.29 4.03 1.31e+00 5.83e-01 9.45e+00 angle pdb=" N GLY E 353 " pdb=" CA GLY E 353 " pdb=" C GLY E 353 " ideal model delta sigma weight residual 115.32 111.33 3.99 1.31e+00 5.83e-01 9.30e+00 angle pdb=" N GLY D 353 " pdb=" CA GLY D 353 " pdb=" C GLY D 353 " ideal model delta sigma weight residual 115.32 111.33 3.99 1.31e+00 5.83e-01 9.27e+00 ... (remaining 17550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6794 17.97 - 35.95: 823 35.95 - 53.92: 218 53.92 - 71.89: 50 71.89 - 89.87: 15 Dihedral angle restraints: 7900 sinusoidal: 3270 harmonic: 4630 Sorted by residual: dihedral pdb=" CB GLU E 110 " pdb=" CG GLU E 110 " pdb=" CD GLU E 110 " pdb=" OE1 GLU E 110 " ideal model delta sinusoidal sigma weight residual 0.00 89.87 -89.87 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 110 " pdb=" CG GLU A 110 " pdb=" CD GLU A 110 " pdb=" OE1 GLU A 110 " ideal model delta sinusoidal sigma weight residual 0.00 89.85 -89.85 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU C 110 " pdb=" CG GLU C 110 " pdb=" CD GLU C 110 " pdb=" OE1 GLU C 110 " ideal model delta sinusoidal sigma weight residual 0.00 89.84 -89.84 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1234 0.026 - 0.051: 495 0.051 - 0.077: 204 0.077 - 0.102: 51 0.102 - 0.128: 36 Chirality restraints: 2020 Sorted by residual: chirality pdb=" CA ILE B 126 " pdb=" N ILE B 126 " pdb=" C ILE B 126 " pdb=" CB ILE B 126 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE E 126 " pdb=" N ILE E 126 " pdb=" C ILE E 126 " pdb=" CB ILE E 126 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE D 126 " pdb=" N ILE D 126 " pdb=" C ILE D 126 " pdb=" CB ILE D 126 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 2017 not shown) Planarity restraints: 2230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 145 " -0.064 5.00e-02 4.00e+02 9.61e-02 1.48e+01 pdb=" N PRO C 146 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO C 146 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 146 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 145 " 0.064 5.00e-02 4.00e+02 9.60e-02 1.47e+01 pdb=" N PRO E 146 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO E 146 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO E 146 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 145 " 0.064 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A 146 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.052 5.00e-02 4.00e+02 ... (remaining 2227 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 241 2.68 - 3.23: 11958 3.23 - 3.79: 20225 3.79 - 4.34: 29920 4.34 - 4.90: 48448 Nonbonded interactions: 110792 Sorted by model distance: nonbonded pdb="MG MG E 500 " pdb=" O HOH D 646 " model vdw 2.121 2.170 nonbonded pdb="MG MG A 502 " pdb=" O HOH E 645 " model vdw 2.121 2.170 nonbonded pdb="MG MG D 500 " pdb=" O HOH C 646 " model vdw 2.122 2.170 nonbonded pdb="MG MG C 501 " pdb=" O HOH B 646 " model vdw 2.122 2.170 nonbonded pdb="MG MG B 500 " pdb=" O HOH A 646 " model vdw 2.122 2.170 ... (remaining 110787 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 84 through 400 or resid 501 through 502)) selection = chain 'B' selection = (chain 'C' and (resid 84 through 400 or resid 501 through 502)) selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 29.570 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.810 ------------------------------------------------------------------------------- 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= 0.206 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 *********************** 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 : 1.481 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: 1.3375 time to fit residues: 290.8471 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 : 2.024 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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= 0.231 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 *********************** 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 : 1.615 Fit side-chains REVERT: A 270 VAL cc_start: 0.7250 (OUTLIER) cc_final: 0.6794 (m) REVERT: A 337 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8362 (ttp-110) REVERT: A 363 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7485 (mp) REVERT: B 270 VAL cc_start: 0.7321 (OUTLIER) cc_final: 0.6906 (m) REVERT: B 337 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8228 (ttp-110) REVERT: C 124 MET cc_start: 0.9155 (tpt) cc_final: 0.8885 (tpt) REVERT: C 203 LYS cc_start: 0.8793 (mttt) cc_final: 0.8575 (mttt) REVERT: C 270 VAL cc_start: 0.7317 (OUTLIER) cc_final: 0.7056 (t) REVERT: C 337 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8231 (ttp-110) REVERT: E 124 MET cc_start: 0.9171 (tpt) cc_final: 0.8854 (tpt) REVERT: E 270 VAL cc_start: 0.7272 (OUTLIER) cc_final: 0.6811 (m) REVERT: E 337 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8233 (ttp-110) outliers start: 46 outliers final: 12 residues processed: 213 average time/residue: 1.3343 time to fit residues: 310.0442 Evaluate side-chains 191 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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 363 LEU 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 78 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 152 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 327 ASN B 298 ASN B 327 ASN E 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13000 Z= 0.335 Angle : 0.564 9.383 17555 Z= 0.291 Chirality : 0.041 0.133 2020 Planarity : 0.005 0.052 2230 Dihedral : 4.232 33.500 1710 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.27 % Allowed : 21.49 % 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: 2.28 (0.22), residues: 1575 helix: 2.16 (0.16), residues: 1035 sheet: 1.92 (0.40), residues: 145 loop : -0.41 (0.35), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 196 HIS 0.007 0.001 HIS B 331 PHE 0.019 0.002 PHE E 359 TYR 0.018 0.002 TYR D 299 ARG 0.005 0.000 ARG B 332 *********************** 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 235 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 175 time to evaluate : 1.575 Fit side-chains REVERT: A 337 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8347 (ttp-110) REVERT: B 270 VAL cc_start: 0.7465 (OUTLIER) cc_final: 0.7021 (m) REVERT: B 337 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8263 (ttp-110) REVERT: C 203 LYS cc_start: 0.8803 (mttt) cc_final: 0.8602 (mttt) REVERT: C 387 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7491 (mt) REVERT: D 329 ASP cc_start: 0.8907 (m-30) cc_final: 0.8699 (m-30) REVERT: E 124 MET cc_start: 0.9208 (tpt) cc_final: 0.8871 (tpt) REVERT: E 337 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8254 (ttp-110) outliers start: 60 outliers final: 28 residues processed: 218 average time/residue: 1.1862 time to fit residues: 284.7287 Evaluate side-chains 201 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 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 270 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 342 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 342 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 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 139 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 149 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1576 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= 0.186 Angle : 0.477 8.774 17555 Z= 0.248 Chirality : 0.037 0.132 2020 Planarity : 0.004 0.050 2230 Dihedral : 3.931 28.226 1710 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.27 % Allowed : 21.64 % Favored : 74.09 % 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: 2.59 (0.22), residues: 1575 helix: 2.46 (0.16), residues: 1035 sheet: 1.81 (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 0.012 0.001 TYR D 299 ARG 0.003 0.000 ARG B 332 *********************** 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 236 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 176 time to evaluate : 1.475 Fit side-chains REVERT: A 270 VAL cc_start: 0.7200 (t) cc_final: 0.6935 (t) REVERT: A 337 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8360 (ttp-110) REVERT: B 314 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.8243 (ttm170) REVERT: B 337 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8229 (ttp-110) REVERT: C 124 MET cc_start: 0.9229 (tpt) cc_final: 0.8945 (tpt) REVERT: C 203 LYS cc_start: 0.8786 (mttt) cc_final: 0.8558 (mttt) REVERT: C 270 VAL cc_start: 0.7314 (t) cc_final: 0.7046 (t) REVERT: C 314 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.8167 (mmt-90) REVERT: C 387 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7482 (mt) REVERT: D 210 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7907 (mt) REVERT: D 314 ARG cc_start: 0.8432 (ttm-80) cc_final: 0.8184 (ttm170) REVERT: E 124 MET cc_start: 0.9235 (tpt) cc_final: 0.8706 (tpt) REVERT: E 270 VAL cc_start: 0.7311 (OUTLIER) cc_final: 0.6858 (m) REVERT: E 314 ARG cc_start: 0.8320 (ttm-80) cc_final: 0.8021 (mmt-90) REVERT: E 337 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8190 (ttp-110) outliers start: 60 outliers final: 26 residues processed: 221 average time/residue: 1.2814 time to fit residues: 309.8686 Evaluate side-chains 202 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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 355 MET Chi-restraints excluded: chain A residue 363 LEU 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 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 232 HIS Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 213 GLU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 127 optimal weight: 0.0170 chunk 103 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.0070 chunk 134 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.8042 ------------------------------------------------------------------------------- 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 E 298 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13000 Z= 0.342 Angle : 0.569 9.335 17555 Z= 0.291 Chirality : 0.041 0.135 2020 Planarity : 0.004 0.045 2230 Dihedral : 4.228 33.002 1710 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.91 % Allowed : 21.64 % Favored : 74.45 % 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: 2.29 (0.22), residues: 1575 helix: 2.21 (0.16), residues: 1040 sheet: 1.80 (0.40), residues: 145 loop : -0.54 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 196 HIS 0.007 0.001 HIS B 331 PHE 0.020 0.002 PHE E 359 TYR 0.019 0.002 TYR D 299 ARG 0.005 0.000 ARG E 332 *********************** 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 230 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 175 time to evaluate : 1.609 Fit side-chains REVERT: A 268 LEU cc_start: 0.8468 (mt) cc_final: 0.8230 (mp) REVERT: A 270 VAL cc_start: 0.7291 (t) cc_final: 0.7017 (t) REVERT: A 337 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8357 (ttp-110) REVERT: A 338 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8710 (tt) REVERT: B 337 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8271 (ttp-110) REVERT: C 160 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6494 (mt-10) REVERT: C 265 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7610 (tp) REVERT: C 270 VAL cc_start: 0.7465 (t) cc_final: 0.7232 (t) REVERT: C 314 ARG cc_start: 0.8517 (ttm-80) cc_final: 0.8259 (ttm170) REVERT: C 387 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7494 (mt) REVERT: D 210 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7910 (mt) REVERT: D 314 ARG cc_start: 0.8502 (ttm-80) cc_final: 0.8236 (ttm170) REVERT: E 124 MET cc_start: 0.9218 (tpt) cc_final: 0.8729 (tpt) REVERT: E 270 VAL cc_start: 0.7430 (t) cc_final: 0.6993 (m) REVERT: E 337 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8289 (ttp-110) outliers start: 55 outliers final: 33 residues processed: 215 average time/residue: 1.2782 time to fit residues: 301.1674 Evaluate side-chains 212 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 1.541 ------------------------------------------------------------------------------- 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 355 MET Chi-restraints excluded: chain A residue 363 LEU 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 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 160 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL 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 213 GLU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 400 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 78 optimal weight: 0.6980 chunk 144 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13000 Z= 0.159 Angle : 0.465 8.388 17555 Z= 0.241 Chirality : 0.037 0.134 2020 Planarity : 0.003 0.046 2230 Dihedral : 3.848 26.244 1710 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.27 % Allowed : 22.70 % 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: 2.73 (0.22), residues: 1575 helix: 2.58 (0.16), residues: 1035 sheet: 1.75 (0.40), residues: 145 loop : -0.32 (0.35), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 196 HIS 0.003 0.001 HIS D 331 PHE 0.022 0.001 PHE E 186 TYR 0.009 0.001 TYR D 299 ARG 0.002 0.000 ARG B 332 *********************** 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 224 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 1.673 Fit side-chains REVERT: A 268 LEU cc_start: 0.8395 (mt) cc_final: 0.8160 (mp) REVERT: A 270 VAL cc_start: 0.7222 (t) cc_final: 0.6913 (t) REVERT: A 337 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8354 (ttp-110) REVERT: B 270 VAL cc_start: 0.7448 (t) cc_final: 0.7217 (m) REVERT: B 314 ARG cc_start: 0.8463 (ttm-80) cc_final: 0.8221 (mmt-90) REVERT: B 337 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8221 (ttp-110) REVERT: C 270 VAL cc_start: 0.7388 (t) cc_final: 0.7004 (m) REVERT: C 314 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8102 (mmt-90) REVERT: C 387 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7415 (mt) REVERT: D 270 VAL cc_start: 0.7540 (t) cc_final: 0.7152 (m) REVERT: D 314 ARG cc_start: 0.8448 (ttm-80) cc_final: 0.8187 (ttm170) REVERT: E 124 MET cc_start: 0.9243 (tpt) cc_final: 0.8734 (tpt) REVERT: E 186 PHE cc_start: 0.7811 (t80) cc_final: 0.7608 (t80) REVERT: E 314 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.8027 (mmt-90) REVERT: E 337 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8212 (ttp-110) outliers start: 46 outliers final: 16 residues processed: 213 average time/residue: 1.3139 time to fit residues: 305.9400 Evaluate side-chains 189 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 337 ARG 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 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 337 ARG 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 16 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 126 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 68 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN B 298 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1714 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= 0.205 Angle : 0.492 8.655 17555 Z= 0.253 Chirality : 0.038 0.134 2020 Planarity : 0.004 0.045 2230 Dihedral : 3.738 29.006 1707 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.63 % Allowed : 21.99 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.22), residues: 1575 helix: 2.71 (0.16), residues: 1005 sheet: 1.83 (0.41), residues: 145 loop : -0.80 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 196 HIS 0.004 0.001 HIS B 331 PHE 0.018 0.002 PHE E 186 TYR 0.014 0.002 TYR D 299 ARG 0.002 0.000 ARG B 332 *********************** 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 222 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 1.535 Fit side-chains REVERT: A 228 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6805 (mtt-85) REVERT: A 268 LEU cc_start: 0.8422 (mt) cc_final: 0.8176 (mp) REVERT: A 270 VAL cc_start: 0.7230 (t) cc_final: 0.6963 (t) REVERT: A 337 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8385 (ttp-110) REVERT: A 338 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8644 (tt) REVERT: B 270 VAL cc_start: 0.7537 (t) cc_final: 0.7263 (m) REVERT: B 314 ARG cc_start: 0.8479 (ttm-80) cc_final: 0.8248 (mmt-90) REVERT: B 337 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8224 (ttp-110) REVERT: B 383 MET cc_start: 0.6797 (mmt) cc_final: 0.6368 (mmm) REVERT: C 314 ARG cc_start: 0.8408 (ttm-80) cc_final: 0.8153 (mmt-90) REVERT: C 387 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7464 (mt) REVERT: D 210 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7904 (mt) REVERT: D 270 VAL cc_start: 0.7615 (t) cc_final: 0.7216 (m) REVERT: D 314 ARG cc_start: 0.8469 (ttm-80) cc_final: 0.8210 (ttm170) REVERT: E 124 MET cc_start: 0.9249 (tpt) cc_final: 0.8739 (tpt) REVERT: E 186 PHE cc_start: 0.7858 (t80) cc_final: 0.7657 (t80) REVERT: E 314 ARG cc_start: 0.8303 (ttm-80) cc_final: 0.8029 (mmt-90) REVERT: E 337 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8325 (ttp-110) outliers start: 51 outliers final: 25 residues processed: 210 average time/residue: 1.2825 time to fit residues: 294.9525 Evaluate side-chains 200 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 228 ARG 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 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 219 VAL Chi-restraints excluded: chain C residue 232 HIS 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 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 400 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.0980 chunk 89 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 0.0670 chunk 117 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN B 298 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN D 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13000 Z= 0.217 Angle : 0.501 8.702 17555 Z= 0.258 Chirality : 0.038 0.133 2020 Planarity : 0.004 0.044 2230 Dihedral : 3.759 29.335 1707 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.20 % Allowed : 22.70 % Favored : 74.09 % 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: 2.60 (0.21), residues: 1575 helix: 2.68 (0.16), residues: 1005 sheet: 1.85 (0.41), residues: 145 loop : -0.79 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 196 HIS 0.005 0.001 HIS B 331 PHE 0.017 0.001 PHE E 186 TYR 0.014 0.002 TYR D 299 ARG 0.003 0.000 ARG B 332 *********************** 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 212 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 1.536 Fit side-chains REVERT: A 228 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6742 (mtt-85) REVERT: A 268 LEU cc_start: 0.8420 (mt) cc_final: 0.8190 (mp) REVERT: A 270 VAL cc_start: 0.7274 (t) cc_final: 0.6977 (t) REVERT: A 337 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8400 (ttp-110) REVERT: A 338 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8670 (tt) REVERT: B 270 VAL cc_start: 0.7545 (t) cc_final: 0.7155 (m) REVERT: B 314 ARG cc_start: 0.8489 (ttm-80) cc_final: 0.8252 (ttm170) REVERT: B 337 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8224 (ttp-110) REVERT: C 314 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.8168 (mmt-90) REVERT: C 387 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7471 (mt) REVERT: D 210 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7901 (mt) REVERT: D 270 VAL cc_start: 0.7620 (t) cc_final: 0.7191 (m) REVERT: D 314 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.8218 (ttm170) REVERT: E 124 MET cc_start: 0.9261 (tpt) cc_final: 0.8744 (tpt) REVERT: E 314 ARG cc_start: 0.8314 (ttm-80) cc_final: 0.8033 (mmt-90) REVERT: E 337 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8334 (ttp-110) outliers start: 45 outliers final: 27 residues processed: 199 average time/residue: 1.3461 time to fit residues: 292.6775 Evaluate side-chains 199 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 1.724 ------------------------------------------------------------------------------- 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 228 ARG 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 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 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 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 343 THR 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 400 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 109 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 chunk 125 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 chunk 138 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 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 B 327 ASN C 298 ASN D 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1737 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= 0.215 Angle : 0.504 8.713 17555 Z= 0.259 Chirality : 0.038 0.133 2020 Planarity : 0.004 0.045 2230 Dihedral : 3.750 29.055 1707 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.85 % Allowed : 22.92 % 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: 2.59 (0.21), residues: 1575 helix: 2.68 (0.16), residues: 1005 sheet: 1.85 (0.41), residues: 145 loop : -0.81 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 196 HIS 0.004 0.001 HIS D 331 PHE 0.020 0.001 PHE A 186 TYR 0.014 0.002 TYR D 299 ARG 0.003 0.000 ARG B 332 *********************** 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 203 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 1.498 Fit side-chains REVERT: A 228 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6728 (mtt-85) REVERT: A 268 LEU cc_start: 0.8417 (mt) cc_final: 0.8184 (mp) REVERT: A 270 VAL cc_start: 0.7279 (t) cc_final: 0.6993 (t) REVERT: A 337 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8383 (ttp-110) REVERT: A 338 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8662 (tt) REVERT: B 270 VAL cc_start: 0.7523 (t) cc_final: 0.7114 (m) REVERT: B 314 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8249 (ttm170) REVERT: B 337 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8214 (ttp-110) REVERT: B 383 MET cc_start: 0.6831 (mmt) cc_final: 0.6408 (mmm) REVERT: C 314 ARG cc_start: 0.8460 (ttm-80) cc_final: 0.8175 (mmt-90) REVERT: C 387 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7487 (mt) REVERT: D 210 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7900 (mt) REVERT: D 270 VAL cc_start: 0.7605 (t) cc_final: 0.7199 (m) REVERT: D 314 ARG cc_start: 0.8460 (ttm-80) cc_final: 0.8214 (ttm170) REVERT: E 124 MET cc_start: 0.9250 (tpt) cc_final: 0.8736 (tpt) REVERT: E 314 ARG cc_start: 0.8306 (ttm-80) cc_final: 0.8036 (mmt-90) REVERT: E 337 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8330 (ttp-110) outliers start: 40 outliers final: 27 residues processed: 193 average time/residue: 1.3243 time to fit residues: 279.1131 Evaluate side-chains 198 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 228 ARG 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 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 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 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 343 THR 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 400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 0.9990 chunk 89 optimal weight: 0.0170 chunk 69 optimal weight: 0.8980 chunk 102 optimal weight: 0.0170 chunk 154 optimal weight: 0.8980 chunk 142 optimal weight: 0.3980 chunk 122 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 94 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13000 Z= 0.147 Angle : 0.454 8.139 17555 Z= 0.236 Chirality : 0.036 0.132 2020 Planarity : 0.003 0.046 2230 Dihedral : 3.530 25.666 1707 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.21 % Allowed : 23.56 % 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: 2.84 (0.21), residues: 1575 helix: 2.93 (0.16), residues: 1005 sheet: 1.82 (0.40), residues: 145 loop : -0.81 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 196 HIS 0.002 0.001 HIS A 223 PHE 0.024 0.001 PHE E 186 TYR 0.008 0.001 TYR E 299 ARG 0.002 0.000 ARG D 136 ********************** 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 204 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 1.519 Fit side-chains REVERT: A 228 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6520 (mtt-85) REVERT: A 337 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8362 (ttp-110) REVERT: A 338 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8660 (tt) REVERT: B 270 VAL cc_start: 0.7496 (t) cc_final: 0.7073 (m) REVERT: B 314 ARG cc_start: 0.8433 (ttm-80) cc_final: 0.8208 (mmt-90) REVERT: B 337 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8237 (ttp-110) REVERT: B 383 MET cc_start: 0.6792 (mmt) cc_final: 0.6379 (mmm) REVERT: C 314 ARG cc_start: 0.8441 (ttm-80) cc_final: 0.8186 (mmt-90) REVERT: C 387 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7479 (mt) REVERT: D 314 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.8155 (mmt-90) REVERT: E 110 GLU cc_start: 0.7552 (tp30) cc_final: 0.7104 (tp30) REVERT: E 124 MET cc_start: 0.9219 (tpt) cc_final: 0.8686 (tpt) REVERT: E 337 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8265 (ttp-110) outliers start: 31 outliers final: 15 residues processed: 199 average time/residue: 1.3365 time to fit residues: 290.1065 Evaluate side-chains 179 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 228 ARG 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 210 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 C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 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 130 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 C 327 ASN D 121 GLN E 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.190851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.122699 restraints weight = 11810.628| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.89 r_work: 0.3006 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13000 Z= 0.407 Angle : 0.618 9.626 17555 Z= 0.313 Chirality : 0.043 0.137 2020 Planarity : 0.004 0.044 2230 Dihedral : 3.866 14.105 1705 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.21 % Allowed : 24.06 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.21), residues: 1575 helix: 2.35 (0.16), residues: 1005 sheet: 1.91 (0.42), residues: 145 loop : -0.83 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 196 HIS 0.009 0.002 HIS B 331 PHE 0.023 0.002 PHE E 186 TYR 0.019 0.003 TYR D 299 ARG 0.008 0.001 ARG E 332 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5171.69 seconds wall clock time: 93 minutes 15.16 seconds (5595.16 seconds total)