Starting phenix.real_space_refine on Sat Jun 7 18:01:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j3x_61127/06_2025/9j3x_61127_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j3x_61127/06_2025/9j3x_61127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j3x_61127/06_2025/9j3x_61127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j3x_61127/06_2025/9j3x_61127.map" model { file = "/net/cci-nas-00/data/ceres_data/9j3x_61127/06_2025/9j3x_61127_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j3x_61127/06_2025/9j3x_61127_neut.cif" } resolution = 3.3 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= 0.000 sd= 0.016 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 P 6 5.49 5 S 46 5.16 5 C 5934 2.51 5 N 1372 2.21 5 O 1536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8894 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4264 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 555} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 110 Chain: "A" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 183 Unusual residues: {'CLR': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B Time building chain proxies: 8.31, per 1000 atoms: 0.93 Number of scatterers: 8894 At special positions: 0 Unit cell: (125.19, 97.37, 72.76, 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 46 16.00 P 6 15.00 O 1536 8.00 N 1372 7.00 C 5934 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 Links applied NAG-ASN " NAG A 905 " - " ASN A 309 " " NAG B 905 " - " ASN B 309 " Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 85.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 38 through 41 Processing helix chain 'A' and resid 42 through 63 removed outlier: 3.536A pdb=" N PHE A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A 53 " --> pdb=" O CYS A 49 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 80 Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.623A pdb=" N ALA A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 125 removed outlier: 3.842A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 141 Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.585A pdb=" N ILE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 165 Processing helix chain 'A' and resid 166 through 197 removed outlier: 4.436A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Proline residue: A 174 - end of helix Proline residue: A 182 - end of helix removed outlier: 3.621A pdb=" N PHE A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP A 195 " --> pdb=" O GLN A 191 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.669A pdb=" N ILE A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.506A pdb=" N PHE A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 250 removed outlier: 4.449A pdb=" N ASN A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.853A pdb=" N SER A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 302 removed outlier: 4.350A pdb=" N LEU A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.705A pdb=" N GLY A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 322 " --> pdb=" O PHE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 337 removed outlier: 4.412A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.899A pdb=" N PHE A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix removed outlier: 4.191A pdb=" N TYR A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 404 removed outlier: 4.272A pdb=" N TYR A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 436 removed outlier: 3.536A pdb=" N THR A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 436 " --> pdb=" O TRP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 473 removed outlier: 3.841A pdb=" N GLY A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 503 Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.736A pdb=" N PHE A 514 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 515 " --> pdb=" O SER A 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 511 through 515' Processing helix chain 'A' and resid 517 through 546 removed outlier: 3.594A pdb=" N MET A 521 " --> pdb=" O GLY A 517 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 682 removed outlier: 3.635A pdb=" N VAL A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU A 660 " --> pdb=" O THR A 656 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 666 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 667 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS A 676 " --> pdb=" O ASN A 672 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 680 " --> pdb=" O CYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 702 Processing helix chain 'A' and resid 702 through 711 Processing helix chain 'B' and resid 38 through 41 Processing helix chain 'B' and resid 42 through 63 removed outlier: 3.536A pdb=" N PHE B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL B 53 " --> pdb=" O CYS B 49 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 80 Processing helix chain 'B' and resid 80 through 92 removed outlier: 3.624A pdb=" N ALA B 84 " --> pdb=" O PHE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 125 removed outlier: 3.842A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 141 Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 149 through 159 removed outlier: 3.586A pdb=" N ILE B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 165 Processing helix chain 'B' and resid 166 through 197 removed outlier: 4.436A pdb=" N TYR B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Proline residue: B 174 - end of helix Proline residue: B 182 - end of helix removed outlier: 3.621A pdb=" N PHE B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR B 196 " --> pdb=" O LYS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 removed outlier: 3.670A pdb=" N ILE B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.507A pdb=" N PHE B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 250 removed outlier: 4.449A pdb=" N ASN B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE B 244 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 264 removed outlier: 3.854A pdb=" N SER B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 302 removed outlier: 4.351A pdb=" N LEU B 290 " --> pdb=" O LYS B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.705A pdb=" N GLY B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 322 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 337 removed outlier: 4.413A pdb=" N ALA B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 367 removed outlier: 3.899A pdb=" N PHE B 352 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Proline residue: B 356 - end of helix removed outlier: 4.192A pdb=" N TYR B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 404 removed outlier: 4.272A pdb=" N TYR B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL B 389 " --> pdb=" O ASP B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 436 removed outlier: 3.536A pdb=" N THR B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 436 " --> pdb=" O TRP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 473 removed outlier: 3.841A pdb=" N GLY B 462 " --> pdb=" O TYR B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 503 Proline residue: B 492 - end of helix Processing helix chain 'B' and resid 511 through 515 removed outlier: 3.737A pdb=" N PHE B 514 " --> pdb=" O ASP B 511 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B 515 " --> pdb=" O SER B 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 511 through 515' Processing helix chain 'B' and resid 517 through 546 removed outlier: 3.594A pdb=" N MET B 521 " --> pdb=" O GLY B 517 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 682 removed outlier: 3.635A pdb=" N VAL B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU B 660 " --> pdb=" O THR B 656 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 665 " --> pdb=" O LEU B 661 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 666 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 667 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS B 676 " --> pdb=" O ASN B 672 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 680 " --> pdb=" O CYS B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 702 Processing helix chain 'B' and resid 702 through 711 662 hydrogen bonds defined for protein. 1974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1340 1.30 - 1.43: 2346 1.43 - 1.56: 5306 1.56 - 1.68: 24 1.68 - 1.81: 74 Bond restraints: 9090 Sorted by residual: bond pdb=" CA GLN A 143 " pdb=" C GLN A 143 " ideal model delta sigma weight residual 1.525 1.434 0.091 1.29e-02 6.01e+03 4.94e+01 bond pdb=" CA GLN B 143 " pdb=" C GLN B 143 " ideal model delta sigma weight residual 1.525 1.435 0.090 1.29e-02 6.01e+03 4.86e+01 bond pdb=" C ASP B 146 " pdb=" O ASP B 146 " ideal model delta sigma weight residual 1.236 1.175 0.061 1.28e-02 6.10e+03 2.25e+01 bond pdb=" C ASP A 146 " pdb=" O ASP A 146 " ideal model delta sigma weight residual 1.236 1.175 0.061 1.28e-02 6.10e+03 2.25e+01 bond pdb=" C GLN B 143 " pdb=" O GLN B 143 " ideal model delta sigma weight residual 1.234 1.177 0.056 1.19e-02 7.06e+03 2.24e+01 ... (remaining 9085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 11999 2.94 - 5.87: 282 5.87 - 8.81: 69 8.81 - 11.74: 2 11.74 - 14.68: 4 Bond angle restraints: 12356 Sorted by residual: angle pdb=" O ALA B 62 " pdb=" C ALA B 62 " pdb=" N ASN B 63 " ideal model delta sigma weight residual 122.08 129.89 -7.81 1.07e+00 8.73e-01 5.32e+01 angle pdb=" O ALA A 62 " pdb=" C ALA A 62 " pdb=" N ASN A 63 " ideal model delta sigma weight residual 122.08 129.76 -7.68 1.07e+00 8.73e-01 5.16e+01 angle pdb=" CA LYS B 269 " pdb=" CB LYS B 269 " pdb=" CG LYS B 269 " ideal model delta sigma weight residual 114.10 128.42 -14.32 2.00e+00 2.50e-01 5.13e+01 angle pdb=" CA LYS A 269 " pdb=" CB LYS A 269 " pdb=" CG LYS A 269 " ideal model delta sigma weight residual 114.10 128.38 -14.28 2.00e+00 2.50e-01 5.10e+01 angle pdb=" N ASN A 198 " pdb=" CA ASN A 198 " pdb=" C ASN A 198 " ideal model delta sigma weight residual 113.61 105.40 8.21 1.50e+00 4.44e-01 2.99e+01 ... (remaining 12351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.75: 4879 22.75 - 45.50: 455 45.50 - 68.26: 94 68.26 - 91.01: 20 91.01 - 113.76: 32 Dihedral angle restraints: 5480 sinusoidal: 2126 harmonic: 3354 Sorted by residual: dihedral pdb=" N2 NAG B 905 " pdb=" C1 NAG B 905 " pdb=" C2 NAG B 905 " pdb=" O5 NAG B 905 " ideal model delta sinusoidal sigma weight residual -178.19 -64.43 -113.76 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" N2 NAG A 905 " pdb=" C1 NAG A 905 " pdb=" C2 NAG A 905 " pdb=" O5 NAG A 905 " ideal model delta sinusoidal sigma weight residual -178.19 -64.47 -113.72 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" C3 NAG B 905 " pdb=" C1 NAG B 905 " pdb=" C2 NAG B 905 " pdb=" O5 NAG B 905 " ideal model delta sinusoidal sigma weight residual -55.55 57.70 -113.25 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 5477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1145 0.062 - 0.124: 264 0.124 - 0.185: 41 0.185 - 0.247: 10 0.247 - 0.309: 6 Chirality restraints: 1466 Sorted by residual: chirality pdb=" C1 NAG B 905 " pdb=" ND2 ASN B 309 " pdb=" C2 NAG B 905 " pdb=" O5 NAG B 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C1 NAG A 905 " pdb=" ND2 ASN A 309 " pdb=" C2 NAG A 905 " pdb=" O5 NAG A 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA ASP B 146 " pdb=" N ASP B 146 " pdb=" C ASP B 146 " pdb=" CB ASP B 146 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 1463 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 371 " -0.057 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO A 372 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 372 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 372 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 371 " 0.056 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO B 372 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 372 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 372 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 367 " 0.052 5.00e-02 4.00e+02 7.89e-02 9.96e+00 pdb=" N PRO B 368 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 368 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 368 " 0.044 5.00e-02 4.00e+02 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2025 2.78 - 3.31: 8354 3.31 - 3.84: 14802 3.84 - 4.37: 16538 4.37 - 4.90: 29258 Nonbonded interactions: 70977 Sorted by model distance: nonbonded pdb=" O SER A 101 " pdb=" OG SER A 105 " model vdw 2.249 3.040 nonbonded pdb=" O SER B 101 " pdb=" OG SER B 105 " model vdw 2.250 3.040 nonbonded pdb=" O SER B 383 " pdb=" OG SER B 387 " model vdw 2.254 3.040 nonbonded pdb=" O SER A 383 " pdb=" OG SER A 387 " model vdw 2.255 3.040 nonbonded pdb=" O ILE B 357 " pdb=" OG SER B 361 " model vdw 2.276 3.040 ... (remaining 70972 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.890 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.810 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 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 : 0.007 0.091 9092 Z= 0.367 Angle : 1.120 14.679 12362 Z= 0.618 Chirality : 0.058 0.309 1466 Planarity : 0.009 0.086 1494 Dihedral : 20.906 113.760 3316 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.44 % Favored : 97.39 % Rotamer: Outliers : 1.67 % Allowed : 22.91 % Favored : 75.42 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.22), residues: 1148 helix: -0.72 (0.15), residues: 898 sheet: None (None), residues: 0 loop : -1.67 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 363 HIS 0.003 0.001 HIS A 310 PHE 0.035 0.003 PHE B 221 TYR 0.034 0.003 TYR A 165 ARG 0.014 0.001 ARG B 270 Details of bonding type rmsd link_NAG-ASN : bond 0.01626 ( 2) link_NAG-ASN : angle 4.66392 ( 6) hydrogen bonds : bond 0.13508 ( 662) hydrogen bonds : angle 6.25080 ( 1974) covalent geometry : bond 0.00717 ( 9090) covalent geometry : angle 1.11604 (12356) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 250 time to evaluate : 0.959 Fit side-chains REVERT: A 97 ASN cc_start: 0.7141 (m-40) cc_final: 0.6870 (p0) REVERT: A 205 LYS cc_start: 0.7190 (tptp) cc_final: 0.6825 (pttt) REVERT: A 276 PHE cc_start: 0.7699 (t80) cc_final: 0.7480 (t80) REVERT: A 409 GLN cc_start: 0.5305 (mp10) cc_final: 0.4488 (pt0) REVERT: A 429 MET cc_start: 0.6106 (tpp) cc_final: 0.5833 (mmt) REVERT: A 430 MET cc_start: 0.4527 (mmt) cc_final: 0.1596 (ptt) REVERT: A 657 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8006 (mtt-85) REVERT: A 670 PHE cc_start: 0.6494 (t80) cc_final: 0.6210 (t80) REVERT: B 114 PHE cc_start: 0.7831 (t80) cc_final: 0.7618 (t80) REVERT: B 674 SER cc_start: 0.8465 (m) cc_final: 0.8225 (p) REVERT: B 705 PHE cc_start: 0.8034 (t80) cc_final: 0.7774 (t80) outliers start: 14 outliers final: 3 residues processed: 257 average time/residue: 0.2147 time to fit residues: 75.3758 Evaluate side-chains 185 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 181 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 61 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 0.0030 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 0.0570 chunk 54 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.5310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.204501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.166645 restraints weight = 11233.480| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.24 r_work: 0.3807 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9092 Z= 0.146 Angle : 0.660 10.984 12362 Z= 0.332 Chirality : 0.043 0.241 1466 Planarity : 0.005 0.062 1494 Dihedral : 15.409 102.230 1622 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.00 % Favored : 97.82 % Rotamer: Outliers : 3.22 % Allowed : 22.20 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.80 (0.25), residues: 1148 helix: 1.11 (0.17), residues: 904 sheet: None (None), residues: 0 loop : -1.54 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 678 HIS 0.003 0.001 HIS A 412 PHE 0.023 0.002 PHE B 221 TYR 0.038 0.001 TYR A 104 ARG 0.003 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00987 ( 2) link_NAG-ASN : angle 4.17560 ( 6) hydrogen bonds : bond 0.04157 ( 662) hydrogen bonds : angle 4.27453 ( 1974) covalent geometry : bond 0.00301 ( 9090) covalent geometry : angle 0.65422 (12356) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.966 Fit side-chains REVERT: A 63 ASN cc_start: 0.8824 (t0) cc_final: 0.8460 (m-40) REVERT: A 97 ASN cc_start: 0.7465 (m-40) cc_final: 0.7049 (p0) REVERT: A 103 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6703 (mt) REVERT: A 155 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8079 (tm-30) REVERT: A 159 GLN cc_start: 0.8369 (tt0) cc_final: 0.8062 (tt0) REVERT: A 170 TYR cc_start: 0.8189 (m-80) cc_final: 0.7223 (m-80) REVERT: A 205 LYS cc_start: 0.7182 (tptp) cc_final: 0.6851 (pttt) REVERT: A 316 TYR cc_start: 0.8142 (t80) cc_final: 0.7917 (t80) REVERT: A 409 GLN cc_start: 0.5443 (mp10) cc_final: 0.4761 (pt0) REVERT: A 430 MET cc_start: 0.5091 (mmt) cc_final: 0.1659 (ptt) REVERT: A 657 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7702 (mtt-85) REVERT: B 299 GLU cc_start: 0.7264 (mm-30) cc_final: 0.7020 (mm-30) REVERT: B 338 MET cc_start: 0.7752 (ptp) cc_final: 0.7505 (ptt) REVERT: B 358 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.7033 (mtm) REVERT: B 413 MET cc_start: 0.5624 (mmm) cc_final: 0.5414 (mmm) REVERT: B 417 ASN cc_start: 0.7184 (m-40) cc_final: 0.6290 (t0) REVERT: B 460 TRP cc_start: 0.6938 (m100) cc_final: 0.6646 (m100) outliers start: 27 outliers final: 9 residues processed: 211 average time/residue: 0.1808 time to fit residues: 54.6327 Evaluate side-chains 180 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 658 HIS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 688 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 44 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 310 HIS A 412 HIS B 412 HIS B 658 HIS ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.187374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.147037 restraints weight = 11495.866| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.31 r_work: 0.3600 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9092 Z= 0.221 Angle : 0.716 12.145 12362 Z= 0.356 Chirality : 0.045 0.176 1466 Planarity : 0.005 0.057 1494 Dihedral : 14.550 96.146 1616 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.79 % Favored : 97.04 % Rotamer: Outliers : 5.49 % Allowed : 21.48 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1148 helix: 1.55 (0.17), residues: 904 sheet: None (None), residues: 0 loop : -1.54 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 193 HIS 0.006 0.001 HIS A 412 PHE 0.029 0.002 PHE B 221 TYR 0.039 0.002 TYR A 104 ARG 0.002 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 2) link_NAG-ASN : angle 3.95156 ( 6) hydrogen bonds : bond 0.04788 ( 662) hydrogen bonds : angle 4.30286 ( 1974) covalent geometry : bond 0.00529 ( 9090) covalent geometry : angle 0.71045 (12356) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8990 (t0) cc_final: 0.8581 (m-40) REVERT: A 71 LYS cc_start: 0.8174 (ttmt) cc_final: 0.7818 (tppt) REVERT: A 97 ASN cc_start: 0.7861 (m-40) cc_final: 0.7250 (p0) REVERT: A 155 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7848 (tm-30) REVERT: A 159 GLN cc_start: 0.8252 (tt0) cc_final: 0.7864 (mt0) REVERT: A 170 TYR cc_start: 0.8348 (m-80) cc_final: 0.8019 (m-80) REVERT: A 217 ASN cc_start: 0.8068 (t0) cc_final: 0.7797 (m110) REVERT: A 269 LYS cc_start: 0.7751 (mmtp) cc_final: 0.7353 (mmtp) REVERT: A 273 LYS cc_start: 0.6201 (ttpp) cc_final: 0.5827 (pttt) REVERT: A 405 LYS cc_start: 0.7483 (mmtt) cc_final: 0.7200 (mttt) REVERT: A 409 GLN cc_start: 0.5729 (mp10) cc_final: 0.4749 (pt0) REVERT: B 177 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8468 (tt) REVERT: B 297 MET cc_start: 0.7630 (mmt) cc_final: 0.7353 (mmt) REVERT: B 299 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7354 (mm-30) REVERT: B 302 ASP cc_start: 0.5867 (OUTLIER) cc_final: 0.5438 (t70) REVERT: B 338 MET cc_start: 0.7942 (ptp) cc_final: 0.7710 (ptt) REVERT: B 417 ASN cc_start: 0.7255 (m-40) cc_final: 0.6394 (t0) REVERT: B 460 TRP cc_start: 0.7194 (m100) cc_final: 0.6731 (m100) REVERT: B 674 SER cc_start: 0.8449 (m) cc_final: 0.8127 (t) outliers start: 46 outliers final: 16 residues processed: 215 average time/residue: 0.2059 time to fit residues: 61.7247 Evaluate side-chains 181 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 688 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 0.0770 chunk 85 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 47 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 HIS ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.192267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.153135 restraints weight = 11288.934| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.26 r_work: 0.3654 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9092 Z= 0.128 Angle : 0.620 12.200 12362 Z= 0.306 Chirality : 0.042 0.174 1466 Planarity : 0.005 0.057 1494 Dihedral : 13.210 93.973 1612 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.61 % Favored : 97.21 % Rotamer: Outliers : 3.10 % Allowed : 23.39 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.02 (0.26), residues: 1148 helix: 2.04 (0.18), residues: 904 sheet: None (None), residues: 0 loop : -1.40 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 679 HIS 0.009 0.001 HIS A 716 PHE 0.024 0.001 PHE B 221 TYR 0.041 0.001 TYR A 104 ARG 0.002 0.000 ARG A 657 Details of bonding type rmsd link_NAG-ASN : bond 0.00663 ( 2) link_NAG-ASN : angle 3.77155 ( 6) hydrogen bonds : bond 0.03939 ( 662) hydrogen bonds : angle 3.98973 ( 1974) covalent geometry : bond 0.00278 ( 9090) covalent geometry : angle 0.61412 (12356) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7843 (ttmt) cc_final: 0.7446 (tppt) REVERT: A 97 ASN cc_start: 0.7642 (m-40) cc_final: 0.7375 (p0) REVERT: A 155 GLU cc_start: 0.8273 (tm-30) cc_final: 0.8035 (tm-30) REVERT: A 170 TYR cc_start: 0.8171 (m-80) cc_final: 0.7762 (m-80) REVERT: A 303 LYS cc_start: 0.6609 (mttt) cc_final: 0.5661 (mmtp) REVERT: A 409 GLN cc_start: 0.5736 (mp10) cc_final: 0.4918 (pt0) REVERT: B 284 THR cc_start: 0.7999 (m) cc_final: 0.7747 (m) REVERT: B 297 MET cc_start: 0.7613 (mmt) cc_final: 0.7373 (mmt) REVERT: B 413 MET cc_start: 0.5130 (mmm) cc_final: 0.4811 (mmm) REVERT: B 417 ASN cc_start: 0.7180 (m-40) cc_final: 0.6302 (t0) REVERT: B 460 TRP cc_start: 0.7036 (m100) cc_final: 0.6603 (m100) outliers start: 26 outliers final: 13 residues processed: 196 average time/residue: 0.1949 time to fit residues: 54.4797 Evaluate side-chains 168 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 713 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 86 optimal weight: 0.8980 chunk 54 optimal weight: 0.2980 chunk 98 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 3 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 HIS ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.189727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150176 restraints weight = 11342.390| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.27 r_work: 0.3634 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9092 Z= 0.136 Angle : 0.627 13.020 12362 Z= 0.308 Chirality : 0.042 0.174 1466 Planarity : 0.004 0.058 1494 Dihedral : 12.674 92.529 1612 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.53 % Favored : 97.30 % Rotamer: Outliers : 2.63 % Allowed : 23.75 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.17 (0.26), residues: 1148 helix: 2.17 (0.18), residues: 904 sheet: None (None), residues: 0 loop : -1.45 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 679 HIS 0.002 0.000 HIS A 716 PHE 0.024 0.001 PHE B 221 TYR 0.038 0.001 TYR A 104 ARG 0.002 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 2) link_NAG-ASN : angle 3.61748 ( 6) hydrogen bonds : bond 0.03970 ( 662) hydrogen bonds : angle 3.91724 ( 1974) covalent geometry : bond 0.00305 ( 9090) covalent geometry : angle 0.62243 (12356) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7876 (ttmt) cc_final: 0.7467 (tppt) REVERT: A 97 ASN cc_start: 0.7628 (m-40) cc_final: 0.7331 (p0) REVERT: A 170 TYR cc_start: 0.8154 (m-80) cc_final: 0.7717 (m-80) REVERT: A 203 LYS cc_start: 0.7768 (mmtt) cc_final: 0.7489 (tptp) REVERT: A 303 LYS cc_start: 0.6557 (mttt) cc_final: 0.5627 (mmtp) REVERT: A 409 GLN cc_start: 0.6005 (mp10) cc_final: 0.5204 (pt0) REVERT: B 297 MET cc_start: 0.7638 (mmt) cc_final: 0.7373 (mmt) REVERT: B 299 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7260 (mm-30) REVERT: B 417 ASN cc_start: 0.7203 (m-40) cc_final: 0.6413 (t0) REVERT: B 460 TRP cc_start: 0.7048 (m100) cc_final: 0.6622 (m100) outliers start: 22 outliers final: 14 residues processed: 187 average time/residue: 0.1930 time to fit residues: 51.2413 Evaluate side-chains 175 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 713 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 97 optimal weight: 0.0020 chunk 109 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.189038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.149744 restraints weight = 11328.687| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.27 r_work: 0.3626 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9092 Z= 0.134 Angle : 0.626 11.794 12362 Z= 0.305 Chirality : 0.042 0.178 1466 Planarity : 0.004 0.060 1494 Dihedral : 12.322 90.531 1612 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.53 % Favored : 97.30 % Rotamer: Outliers : 2.39 % Allowed : 24.58 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.30 (0.26), residues: 1148 helix: 2.25 (0.18), residues: 906 sheet: None (None), residues: 0 loop : -1.40 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 679 HIS 0.002 0.000 HIS A 716 PHE 0.025 0.002 PHE B 221 TYR 0.036 0.001 TYR A 104 ARG 0.002 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 2) link_NAG-ASN : angle 3.55481 ( 6) hydrogen bonds : bond 0.03936 ( 662) hydrogen bonds : angle 3.87267 ( 1974) covalent geometry : bond 0.00303 ( 9090) covalent geometry : angle 0.62137 (12356) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7907 (ttmt) cc_final: 0.7479 (tppt) REVERT: A 170 TYR cc_start: 0.8124 (m-80) cc_final: 0.7678 (m-80) REVERT: A 203 LYS cc_start: 0.7787 (mmtt) cc_final: 0.7523 (tptp) REVERT: A 233 LEU cc_start: 0.7724 (tp) cc_final: 0.7503 (tp) REVERT: A 303 LYS cc_start: 0.6803 (mttt) cc_final: 0.5979 (mmtp) REVERT: A 316 TYR cc_start: 0.8202 (t80) cc_final: 0.7981 (t80) REVERT: A 409 GLN cc_start: 0.6256 (mp10) cc_final: 0.5335 (pt0) REVERT: A 663 LEU cc_start: 0.7483 (tt) cc_final: 0.7168 (mt) REVERT: A 666 ILE cc_start: 0.8082 (pt) cc_final: 0.7835 (mt) REVERT: B 63 ASN cc_start: 0.8197 (t0) cc_final: 0.7900 (t0) REVERT: B 297 MET cc_start: 0.7641 (mmt) cc_final: 0.7372 (mmt) REVERT: B 299 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7305 (mm-30) REVERT: B 417 ASN cc_start: 0.7281 (m-40) cc_final: 0.6446 (t0) REVERT: B 460 TRP cc_start: 0.7049 (m100) cc_final: 0.6622 (m100) REVERT: B 674 SER cc_start: 0.8472 (m) cc_final: 0.8239 (t) outliers start: 20 outliers final: 16 residues processed: 190 average time/residue: 0.1829 time to fit residues: 49.9201 Evaluate side-chains 179 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 658 HIS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 713 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.185132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.145245 restraints weight = 11535.234| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.29 r_work: 0.3601 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9092 Z= 0.160 Angle : 0.655 12.141 12362 Z= 0.322 Chirality : 0.043 0.176 1466 Planarity : 0.004 0.059 1494 Dihedral : 12.396 89.884 1612 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.70 % Favored : 97.13 % Rotamer: Outliers : 2.63 % Allowed : 24.58 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.30 (0.26), residues: 1148 helix: 2.23 (0.18), residues: 904 sheet: None (None), residues: 0 loop : -1.28 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 679 HIS 0.002 0.001 HIS A 716 PHE 0.026 0.002 PHE B 221 TYR 0.035 0.002 TYR A 104 ARG 0.003 0.000 ARG A 657 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 2) link_NAG-ASN : angle 3.44200 ( 6) hydrogen bonds : bond 0.04163 ( 662) hydrogen bonds : angle 3.96480 ( 1974) covalent geometry : bond 0.00376 ( 9090) covalent geometry : angle 0.65045 (12356) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7974 (ttmt) cc_final: 0.7647 (tppt) REVERT: A 170 TYR cc_start: 0.8272 (m-80) cc_final: 0.7894 (m-80) REVERT: A 240 TYR cc_start: 0.8694 (m-10) cc_final: 0.8455 (m-10) REVERT: A 303 LYS cc_start: 0.6755 (mttt) cc_final: 0.6078 (mmtp) REVERT: A 395 ILE cc_start: 0.8172 (mm) cc_final: 0.7794 (mt) REVERT: A 409 GLN cc_start: 0.6374 (mp10) cc_final: 0.5477 (tt0) REVERT: A 663 LEU cc_start: 0.7613 (tt) cc_final: 0.7345 (mt) REVERT: B 63 ASN cc_start: 0.8232 (t0) cc_final: 0.7910 (t0) REVERT: B 284 THR cc_start: 0.7950 (m) cc_final: 0.7692 (m) REVERT: B 297 MET cc_start: 0.7755 (mmt) cc_final: 0.7426 (mmt) REVERT: B 299 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7334 (mm-30) REVERT: B 417 ASN cc_start: 0.7290 (m-40) cc_final: 0.6486 (t0) REVERT: B 460 TRP cc_start: 0.7236 (m100) cc_final: 0.6799 (m100) outliers start: 22 outliers final: 19 residues processed: 185 average time/residue: 0.2144 time to fit residues: 56.4392 Evaluate side-chains 182 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 713 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 27 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 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 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.186792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.147683 restraints weight = 11552.236| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.24 r_work: 0.3622 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9092 Z= 0.147 Angle : 0.645 12.710 12362 Z= 0.314 Chirality : 0.043 0.179 1466 Planarity : 0.004 0.059 1494 Dihedral : 12.270 88.778 1612 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.70 % Favored : 97.13 % Rotamer: Outliers : 3.10 % Allowed : 24.82 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.38 (0.26), residues: 1148 helix: 2.30 (0.18), residues: 902 sheet: None (None), residues: 0 loop : -1.30 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 679 HIS 0.003 0.001 HIS A 658 PHE 0.025 0.002 PHE B 221 TYR 0.037 0.002 TYR A 104 ARG 0.003 0.000 ARG A 657 Details of bonding type rmsd link_NAG-ASN : bond 0.00554 ( 2) link_NAG-ASN : angle 3.54009 ( 6) hydrogen bonds : bond 0.04039 ( 662) hydrogen bonds : angle 3.91986 ( 1974) covalent geometry : bond 0.00341 ( 9090) covalent geometry : angle 0.64024 (12356) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7937 (ttmt) cc_final: 0.7620 (tppt) REVERT: A 170 TYR cc_start: 0.8179 (m-80) cc_final: 0.7804 (m-80) REVERT: A 240 TYR cc_start: 0.8596 (m-10) cc_final: 0.8358 (m-10) REVERT: A 272 LYS cc_start: 0.7456 (tmtt) cc_final: 0.7222 (tmtt) REVERT: A 303 LYS cc_start: 0.6612 (mttt) cc_final: 0.6087 (mmtp) REVERT: A 316 TYR cc_start: 0.8139 (t80) cc_final: 0.7858 (t80) REVERT: A 395 ILE cc_start: 0.8189 (mm) cc_final: 0.7826 (mt) REVERT: A 409 GLN cc_start: 0.6364 (mp10) cc_final: 0.5578 (tt0) REVERT: A 663 LEU cc_start: 0.7621 (tt) cc_final: 0.7202 (mt) REVERT: B 63 ASN cc_start: 0.8195 (t0) cc_final: 0.7895 (t0) REVERT: B 284 THR cc_start: 0.7878 (m) cc_final: 0.7615 (m) REVERT: B 297 MET cc_start: 0.7694 (mmt) cc_final: 0.7393 (mmt) REVERT: B 417 ASN cc_start: 0.7275 (m-40) cc_final: 0.6458 (t0) REVERT: B 460 TRP cc_start: 0.7224 (m100) cc_final: 0.6769 (m100) outliers start: 26 outliers final: 21 residues processed: 188 average time/residue: 0.1920 time to fit residues: 50.9148 Evaluate side-chains 185 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 658 HIS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 713 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 50 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.187886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.148767 restraints weight = 11475.737| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.24 r_work: 0.3610 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9092 Z= 0.134 Angle : 0.645 12.513 12362 Z= 0.315 Chirality : 0.042 0.177 1466 Planarity : 0.004 0.059 1494 Dihedral : 12.174 89.198 1612 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.61 % Favored : 97.21 % Rotamer: Outliers : 2.86 % Allowed : 25.54 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.39 (0.26), residues: 1148 helix: 2.30 (0.18), residues: 908 sheet: None (None), residues: 0 loop : -1.33 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 679 HIS 0.003 0.001 HIS A 658 PHE 0.037 0.002 PHE A 115 TYR 0.025 0.001 TYR B 104 ARG 0.001 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 2) link_NAG-ASN : angle 3.55516 ( 6) hydrogen bonds : bond 0.03923 ( 662) hydrogen bonds : angle 3.87412 ( 1974) covalent geometry : bond 0.00301 ( 9090) covalent geometry : angle 0.64085 (12356) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 1.207 Fit side-chains REVERT: A 71 LYS cc_start: 0.7850 (ttmt) cc_final: 0.7481 (tppt) REVERT: A 170 TYR cc_start: 0.8121 (m-80) cc_final: 0.7709 (m-80) REVERT: A 240 TYR cc_start: 0.8620 (m-10) cc_final: 0.8365 (m-10) REVERT: A 303 LYS cc_start: 0.6657 (mttt) cc_final: 0.6120 (mmtp) REVERT: A 316 TYR cc_start: 0.8115 (t80) cc_final: 0.7880 (t80) REVERT: A 395 ILE cc_start: 0.8129 (mm) cc_final: 0.7775 (mt) REVERT: A 409 GLN cc_start: 0.6382 (mp10) cc_final: 0.5645 (tt0) REVERT: B 63 ASN cc_start: 0.8108 (t0) cc_final: 0.7840 (t0) REVERT: B 297 MET cc_start: 0.7713 (mmt) cc_final: 0.7349 (mmt) REVERT: B 406 LYS cc_start: 0.8325 (tptt) cc_final: 0.7731 (tppt) REVERT: B 417 ASN cc_start: 0.7338 (m-40) cc_final: 0.6467 (t0) REVERT: B 460 TRP cc_start: 0.7214 (m100) cc_final: 0.6766 (m100) outliers start: 24 outliers final: 21 residues processed: 189 average time/residue: 0.2104 time to fit residues: 56.9947 Evaluate side-chains 181 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 658 HIS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 713 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 50 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.183290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.143356 restraints weight = 11356.145| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.36 r_work: 0.3564 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9092 Z= 0.146 Angle : 0.678 15.396 12362 Z= 0.330 Chirality : 0.043 0.178 1466 Planarity : 0.004 0.059 1494 Dihedral : 12.163 87.635 1612 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.79 % Favored : 97.04 % Rotamer: Outliers : 2.86 % Allowed : 25.78 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.30 (0.26), residues: 1148 helix: 2.21 (0.18), residues: 920 sheet: None (None), residues: 0 loop : -1.42 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 679 HIS 0.002 0.000 HIS A 658 PHE 0.035 0.002 PHE A 115 TYR 0.037 0.001 TYR A 104 ARG 0.001 0.000 ARG A 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 2) link_NAG-ASN : angle 3.55047 ( 6) hydrogen bonds : bond 0.04052 ( 662) hydrogen bonds : angle 3.87684 ( 1974) covalent geometry : bond 0.00334 ( 9090) covalent geometry : angle 0.67367 (12356) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.889 Fit side-chains REVERT: A 71 LYS cc_start: 0.7917 (ttmt) cc_final: 0.7480 (tppt) REVERT: A 170 TYR cc_start: 0.8113 (m-80) cc_final: 0.7625 (m-80) REVERT: A 240 TYR cc_start: 0.8537 (m-10) cc_final: 0.8263 (m-10) REVERT: A 303 LYS cc_start: 0.6654 (mttt) cc_final: 0.6074 (mmtp) REVERT: A 395 ILE cc_start: 0.8154 (mm) cc_final: 0.7806 (mt) REVERT: A 409 GLN cc_start: 0.6482 (mp10) cc_final: 0.5712 (tt0) REVERT: A 459 LEU cc_start: 0.8379 (tp) cc_final: 0.8042 (mp) REVERT: A 678 TRP cc_start: 0.8249 (t-100) cc_final: 0.7876 (t60) REVERT: B 63 ASN cc_start: 0.8112 (t0) cc_final: 0.7855 (t0) REVERT: B 297 MET cc_start: 0.7642 (mmt) cc_final: 0.7334 (mmt) REVERT: B 406 LYS cc_start: 0.8414 (tptt) cc_final: 0.7794 (tppt) REVERT: B 417 ASN cc_start: 0.7326 (m-40) cc_final: 0.6514 (t0) REVERT: B 460 TRP cc_start: 0.7209 (m100) cc_final: 0.6789 (m100) outliers start: 24 outliers final: 24 residues processed: 177 average time/residue: 0.1806 time to fit residues: 45.7643 Evaluate side-chains 185 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 658 HIS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 713 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 62 optimal weight: 0.0870 chunk 60 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 108 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.185204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.145468 restraints weight = 11417.975| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.38 r_work: 0.3574 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.6040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9092 Z= 0.129 Angle : 0.667 15.228 12362 Z= 0.324 Chirality : 0.042 0.173 1466 Planarity : 0.004 0.059 1494 Dihedral : 11.895 87.360 1612 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.61 % Favored : 97.21 % Rotamer: Outliers : 2.74 % Allowed : 26.01 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.50 (0.26), residues: 1148 helix: 2.39 (0.18), residues: 906 sheet: None (None), residues: 0 loop : -1.32 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 679 HIS 0.002 0.000 HIS A 658 PHE 0.034 0.001 PHE A 115 TYR 0.044 0.001 TYR A 165 ARG 0.003 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00581 ( 2) link_NAG-ASN : angle 3.64869 ( 6) hydrogen bonds : bond 0.03810 ( 662) hydrogen bonds : angle 3.79468 ( 1974) covalent geometry : bond 0.00284 ( 9090) covalent geometry : angle 0.66211 (12356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4268.14 seconds wall clock time: 75 minutes 35.67 seconds (4535.67 seconds total)