Starting phenix.real_space_refine on Wed Mar 4 17:42:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jsj_22456/03_2026/7jsj_22456_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jsj_22456/03_2026/7jsj_22456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jsj_22456/03_2026/7jsj_22456_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jsj_22456/03_2026/7jsj_22456_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jsj_22456/03_2026/7jsj_22456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jsj_22456/03_2026/7jsj_22456.map" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians S 64 5.16 5 Na 4 4.78 5 C 4940 2.51 5 N 1152 2.21 5 O 1228 1.98 5 H 7668 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15056 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7491 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 29, 'TRANS': 438} Chain breaks: 4 Chain: "B" Number of atoms: 7491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7491 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 29, 'TRANS': 438} Chain breaks: 4 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Unusual residues: {' NA': 2, 'NAG': 1, 'X3M': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Unusual residues: {' NA': 2, 'NAG': 1, 'X3M': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.61, per 1000 atoms: 0.17 Number of scatterers: 15056 At special positions: 0 Unit cell: (85.84, 82.621, 108.373, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 64 16.00 Na 4 11.00 O 1228 8.00 N 1152 7.00 C 4940 6.00 H 7668 1.00 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 601 " - " ASN A 562 " " NAG B 601 " - " ASN B 562 " Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 449.8 milliseconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1780 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 81.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 15 through 19 Processing helix chain 'A' and resid 20 through 29 Proline residue: A 26 - end of helix removed outlier: 3.695A pdb=" N ILE A 29 " --> pdb=" O PRO A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 51 removed outlier: 3.815A pdb=" N ARG A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 84 through 103 removed outlier: 3.668A pdb=" N TRP A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.697A pdb=" N LEU A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 removed outlier: 3.543A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 158 removed outlier: 3.809A pdb=" N THR A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Proline residue: A 150 - end of helix removed outlier: 3.747A pdb=" N GLN A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 220 removed outlier: 3.993A pdb=" N LYS A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 227 through 241 removed outlier: 4.016A pdb=" N VAL A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 276 Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.937A pdb=" N GLU A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 313 through 333 removed outlier: 3.883A pdb=" N ILE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 367 removed outlier: 3.924A pdb=" N VAL A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 Processing helix chain 'A' and resid 408 through 428 removed outlier: 3.580A pdb=" N LEU A 412 " --> pdb=" O TRP A 408 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 436 Processing helix chain 'A' and resid 438 through 442 removed outlier: 3.658A pdb=" N ALA A 442 " --> pdb=" O PRO A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 460 Processing helix chain 'A' and resid 464 through 484 removed outlier: 3.510A pdb=" N THR A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Proline residue: A 474 - end of helix removed outlier: 3.626A pdb=" N SER A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 498 Proline residue: A 493 - end of helix Processing helix chain 'A' and resid 504 through 507 Processing helix chain 'A' and resid 508 through 516 removed outlier: 3.659A pdb=" N ALA A 512 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 547 removed outlier: 3.671A pdb=" N MET A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET A 532 " --> pdb=" O THR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 553 removed outlier: 4.084A pdb=" N ILE A 551 " --> pdb=" O TRP A 547 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 19 Processing helix chain 'B' and resid 20 through 29 Proline residue: B 26 - end of helix removed outlier: 3.695A pdb=" N ILE B 29 " --> pdb=" O PRO B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 51 removed outlier: 3.816A pdb=" N ARG B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 62 through 67 Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 84 through 103 removed outlier: 3.667A pdb=" N TRP B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 118 removed outlier: 3.698A pdb=" N LEU B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 137 removed outlier: 3.544A pdb=" N LEU B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 158 removed outlier: 3.809A pdb=" N THR B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Proline residue: B 150 - end of helix removed outlier: 3.748A pdb=" N GLN B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 220 removed outlier: 3.992A pdb=" N LYS B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 227 through 241 removed outlier: 4.015A pdb=" N VAL B 231 " --> pdb=" O THR B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 276 Proline residue: B 259 - end of helix Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 298 through 307 removed outlier: 3.937A pdb=" N GLU B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 313 through 333 removed outlier: 3.883A pdb=" N ILE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 367 removed outlier: 3.923A pdb=" N VAL B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 405 Processing helix chain 'B' and resid 408 through 428 removed outlier: 3.581A pdb=" N LEU B 412 " --> pdb=" O TRP B 408 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY B 415 " --> pdb=" O VAL B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 436 Processing helix chain 'B' and resid 438 through 442 removed outlier: 3.658A pdb=" N ALA B 442 " --> pdb=" O PRO B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 460 Processing helix chain 'B' and resid 464 through 484 removed outlier: 3.509A pdb=" N THR B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) Proline residue: B 474 - end of helix removed outlier: 3.625A pdb=" N SER B 482 " --> pdb=" O SER B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 498 Proline residue: B 493 - end of helix Processing helix chain 'B' and resid 504 through 507 Processing helix chain 'B' and resid 508 through 516 removed outlier: 3.659A pdb=" N ALA B 512 " --> pdb=" O THR B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 547 removed outlier: 3.671A pdb=" N MET B 525 " --> pdb=" O LYS B 521 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE B 531 " --> pdb=" O LYS B 527 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET B 532 " --> pdb=" O THR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 553 removed outlier: 4.085A pdb=" N ILE B 551 " --> pdb=" O TRP B 547 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1296 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: 3.10 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7648 1.03 - 1.22: 22 1.22 - 1.42: 3016 1.42 - 1.61: 4450 1.61 - 1.81: 108 Bond restraints: 15244 Sorted by residual: bond pdb=" C1 NAG B 601 " pdb=" C2 NAG B 601 " ideal model delta sigma weight residual 1.532 1.599 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C1 NAG A 601 " pdb=" C2 NAG A 601 " ideal model delta sigma weight residual 1.532 1.598 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C7 NAG A 601 " pdb=" N2 NAG A 601 " ideal model delta sigma weight residual 1.346 1.393 -0.047 2.00e-02 2.50e+03 5.50e+00 bond pdb=" C7 NAG B 601 " pdb=" N2 NAG B 601 " ideal model delta sigma weight residual 1.346 1.393 -0.047 2.00e-02 2.50e+03 5.43e+00 bond pdb=" C02 X3M A 602 " pdb=" C05 X3M A 602 " ideal model delta sigma weight residual 1.526 1.487 0.039 2.00e-02 2.50e+03 3.84e+00 ... (remaining 15239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.26: 27500 7.26 - 14.52: 32 14.52 - 21.79: 22 21.79 - 29.05: 136 29.05 - 36.31: 58 Bond angle restraints: 27748 Sorted by residual: angle pdb=" CB VAL A 263 " pdb=" CA VAL A 263 " pdb=" HA VAL A 263 " ideal model delta sigma weight residual 109.00 72.69 36.31 3.00e+00 1.11e-01 1.46e+02 angle pdb=" CB VAL B 263 " pdb=" CA VAL B 263 " pdb=" HA VAL B 263 " ideal model delta sigma weight residual 109.00 72.86 36.14 3.00e+00 1.11e-01 1.45e+02 angle pdb=" C SER B 291 " pdb=" CA SER B 291 " pdb=" HA SER B 291 " ideal model delta sigma weight residual 109.00 73.34 35.66 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C SER A 291 " pdb=" CA SER A 291 " pdb=" HA SER A 291 " ideal model delta sigma weight residual 109.00 73.62 35.38 3.00e+00 1.11e-01 1.39e+02 angle pdb=" N SER A 291 " pdb=" CA SER A 291 " pdb=" HA SER A 291 " ideal model delta sigma weight residual 110.00 74.85 35.15 3.00e+00 1.11e-01 1.37e+02 ... (remaining 27743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 6452 16.55 - 33.10: 491 33.10 - 49.65: 167 49.65 - 66.21: 83 66.21 - 82.76: 9 Dihedral angle restraints: 7202 sinusoidal: 3898 harmonic: 3304 Sorted by residual: dihedral pdb=" CA THR B 225 " pdb=" C THR B 225 " pdb=" N GLY B 226 " pdb=" CA GLY B 226 " ideal model delta harmonic sigma weight residual 180.00 152.59 27.41 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA THR A 225 " pdb=" C THR A 225 " pdb=" N GLY A 226 " pdb=" CA GLY A 226 " ideal model delta harmonic sigma weight residual 180.00 152.60 27.40 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA TYR A 353 " pdb=" C TYR A 353 " pdb=" N VAL A 354 " pdb=" CA VAL A 354 " ideal model delta harmonic sigma weight residual -180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 7199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.345: 1232 0.345 - 0.689: 2 0.689 - 1.034: 0 1.034 - 1.378: 4 1.378 - 1.723: 12 Chirality restraints: 1250 Sorted by residual: chirality pdb=" CG LEU B 27 " pdb=" CB LEU B 27 " pdb=" CD1 LEU B 27 " pdb=" CD2 LEU B 27 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.42e+01 chirality pdb=" CG LEU A 27 " pdb=" CB LEU A 27 " pdb=" CD1 LEU A 27 " pdb=" CD2 LEU A 27 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.36e+01 chirality pdb=" CG LEU A 23 " pdb=" CB LEU A 23 " pdb=" CD1 LEU A 23 " pdb=" CD2 LEU A 23 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.10e+01 ... (remaining 1247 not shown) Planarity restraints: 2106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 406 " -0.031 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO B 407 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 407 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 407 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 406 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO A 407 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 407 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 407 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 310 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO A 311 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 311 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 311 " -0.025 5.00e-02 4.00e+02 ... (remaining 2103 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 841 2.16 - 2.77: 29736 2.77 - 3.38: 41996 3.38 - 3.99: 53957 3.99 - 4.60: 88078 Nonbonded interactions: 214608 Sorted by model distance: nonbonded pdb=" O THR B 225 " pdb=" H THR B 227 " model vdw 1.553 2.450 nonbonded pdb=" O THR A 225 " pdb=" H THR A 227 " model vdw 1.554 2.450 nonbonded pdb=" O MET A 31 " pdb=" H ALA A 33 " model vdw 1.558 2.450 nonbonded pdb=" O MET B 31 " pdb=" H ALA B 33 " model vdw 1.558 2.450 nonbonded pdb=" HA VAL A 263 " pdb=" HB VAL A 263 " model vdw 1.587 1.952 ... (remaining 214603 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: 0.01 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.570 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 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 : 0.008 0.067 7578 Z= 0.304 Angle : 1.100 26.291 10342 Z= 0.483 Chirality : 0.182 1.723 1250 Planarity : 0.005 0.046 1236 Dihedral : 12.914 65.085 2722 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.17 % Favored : 90.61 % Rotamer: Outliers : 7.23 % Allowed : 8.73 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.30), residues: 916 helix: 0.84 (0.21), residues: 682 sheet: None (None), residues: 0 loop : -3.23 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 102 TYR 0.012 0.001 TYR A 353 PHE 0.019 0.001 PHE A 35 TRP 0.010 0.002 TRP A 560 HIS 0.002 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00790 ( 7576) covalent geometry : angle 1.09795 (10336) hydrogen bonds : bond 0.14111 ( 446) hydrogen bonds : angle 5.71546 ( 1296) link_NAG-ASN : bond 0.00865 ( 2) link_NAG-ASN : angle 2.90525 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 102 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6705 (mmt) REVERT: A 240 LEU cc_start: 0.8040 (mt) cc_final: 0.7617 (mt) REVERT: A 312 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6461 (tt) REVERT: A 391 PHE cc_start: 0.4442 (OUTLIER) cc_final: 0.3827 (m-80) REVERT: A 392 TYR cc_start: 0.6859 (OUTLIER) cc_final: 0.5332 (m-80) REVERT: A 458 VAL cc_start: 0.8314 (t) cc_final: 0.8111 (m) REVERT: B 115 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7978 (mt) REVERT: B 158 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6322 (mm-40) REVERT: B 312 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7166 (tt) REVERT: B 369 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7897 (pt) REVERT: B 391 PHE cc_start: 0.4144 (OUTLIER) cc_final: 0.3228 (t80) REVERT: B 392 TYR cc_start: 0.3641 (OUTLIER) cc_final: 0.2582 (m-80) outliers start: 58 outliers final: 18 residues processed: 154 average time/residue: 0.1955 time to fit residues: 40.8194 Evaluate side-chains 109 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 106 HIS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.0870 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.151960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138980 restraints weight = 22647.739| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.58 r_work: 0.3622 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7578 Z= 0.146 Angle : 1.075 26.510 10342 Z= 0.477 Chirality : 0.181 1.734 1250 Planarity : 0.006 0.053 1236 Dihedral : 9.379 87.201 1105 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.31 % Favored : 92.47 % Rotamer: Outliers : 4.11 % Allowed : 11.47 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.30), residues: 916 helix: 1.11 (0.21), residues: 688 sheet: None (None), residues: 0 loop : -3.21 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 108 TYR 0.009 0.001 TYR B 353 PHE 0.018 0.001 PHE B 258 TRP 0.010 0.001 TRP B 49 HIS 0.006 0.001 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 7576) covalent geometry : angle 1.07368 (10336) hydrogen bonds : bond 0.04919 ( 446) hydrogen bonds : angle 4.45766 ( 1296) link_NAG-ASN : bond 0.00973 ( 2) link_NAG-ASN : angle 2.55195 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6238 (tt) REVERT: A 391 PHE cc_start: 0.4621 (OUTLIER) cc_final: 0.4010 (m-80) REVERT: A 392 TYR cc_start: 0.6792 (OUTLIER) cc_final: 0.5423 (m-80) REVERT: B 115 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7774 (mt) REVERT: B 158 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6632 (mm-40) REVERT: B 202 LYS cc_start: 0.6930 (mtmt) cc_final: 0.6658 (tptt) REVERT: B 312 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7203 (tt) REVERT: B 391 PHE cc_start: 0.3661 (OUTLIER) cc_final: 0.2661 (t80) REVERT: B 392 TYR cc_start: 0.3632 (OUTLIER) cc_final: 0.2678 (m-80) REVERT: B 413 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7284 (tt) outliers start: 33 outliers final: 21 residues processed: 114 average time/residue: 0.1497 time to fit residues: 24.7122 Evaluate side-chains 111 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 106 HIS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 63 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.144803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.131356 restraints weight = 23356.835| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.62 r_work: 0.3557 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7578 Z= 0.163 Angle : 1.059 26.235 10342 Z= 0.469 Chirality : 0.182 1.729 1250 Planarity : 0.006 0.054 1236 Dihedral : 9.040 87.357 1096 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 4.36 % Allowed : 12.22 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.30), residues: 916 helix: 1.44 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -2.76 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 108 TYR 0.010 0.001 TYR B 353 PHE 0.016 0.001 PHE B 258 TRP 0.011 0.001 TRP A 49 HIS 0.006 0.001 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 7576) covalent geometry : angle 1.05726 (10336) hydrogen bonds : bond 0.04948 ( 446) hydrogen bonds : angle 4.30436 ( 1296) link_NAG-ASN : bond 0.00790 ( 2) link_NAG-ASN : angle 2.75659 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: 0.7625 (mtt) cc_final: 0.7412 (mtp) REVERT: A 312 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6281 (tt) REVERT: A 391 PHE cc_start: 0.4724 (OUTLIER) cc_final: 0.4053 (m-80) REVERT: A 392 TYR cc_start: 0.6844 (OUTLIER) cc_final: 0.5511 (m-80) REVERT: A 556 HIS cc_start: 0.7477 (m-70) cc_final: 0.7056 (m90) REVERT: B 115 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7827 (mt) REVERT: B 158 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6642 (mm-40) REVERT: B 312 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7287 (tt) REVERT: B 369 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7949 (pt) REVERT: B 391 PHE cc_start: 0.3720 (OUTLIER) cc_final: 0.2634 (t80) REVERT: B 392 TYR cc_start: 0.3728 (OUTLIER) cc_final: 0.2867 (m-80) REVERT: B 413 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7368 (tt) REVERT: B 517 TYR cc_start: 0.8669 (m-80) cc_final: 0.8399 (m-80) outliers start: 35 outliers final: 21 residues processed: 130 average time/residue: 0.1378 time to fit residues: 26.6064 Evaluate side-chains 123 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 106 HIS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 0.2980 chunk 86 optimal weight: 0.0870 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 23 optimal weight: 0.0970 chunk 79 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 71 optimal weight: 0.0870 overall best weight: 0.1734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.160801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.147521 restraints weight = 22261.890| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.56 r_work: 0.3695 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7578 Z= 0.126 Angle : 1.035 26.255 10342 Z= 0.451 Chirality : 0.182 1.732 1250 Planarity : 0.005 0.049 1236 Dihedral : 8.660 84.252 1090 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 4.61 % Allowed : 12.09 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.30), residues: 916 helix: 1.60 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -2.72 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 108 TYR 0.012 0.001 TYR A 517 PHE 0.010 0.001 PHE B 35 TRP 0.010 0.001 TRP A 49 HIS 0.006 0.001 HIS A 556 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7576) covalent geometry : angle 1.03316 (10336) hydrogen bonds : bond 0.04010 ( 446) hydrogen bonds : angle 4.04914 ( 1296) link_NAG-ASN : bond 0.00852 ( 2) link_NAG-ASN : angle 2.74245 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ARG cc_start: 0.6424 (mmm160) cc_final: 0.5921 (mmm160) REVERT: A 312 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6230 (tt) REVERT: A 391 PHE cc_start: 0.4828 (OUTLIER) cc_final: 0.4153 (m-80) REVERT: A 392 TYR cc_start: 0.6763 (OUTLIER) cc_final: 0.5383 (m-10) REVERT: B 115 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7830 (mt) REVERT: B 158 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6467 (mm-40) REVERT: B 239 GLU cc_start: 0.7447 (tp30) cc_final: 0.7199 (mm-30) REVERT: B 312 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7272 (tt) REVERT: B 369 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7958 (pt) REVERT: B 391 PHE cc_start: 0.4004 (OUTLIER) cc_final: 0.2817 (t80) REVERT: B 392 TYR cc_start: 0.3997 (OUTLIER) cc_final: 0.3190 (m-80) REVERT: B 413 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7381 (tt) REVERT: B 517 TYR cc_start: 0.8590 (m-80) cc_final: 0.8318 (m-80) outliers start: 37 outliers final: 24 residues processed: 124 average time/residue: 0.1537 time to fit residues: 27.8376 Evaluate side-chains 126 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 39 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 83 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.153250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.140438 restraints weight = 23120.776| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.55 r_work: 0.3632 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 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 : 0.004 0.056 7578 Z= 0.166 Angle : 1.043 26.220 10342 Z= 0.458 Chirality : 0.182 1.729 1250 Planarity : 0.006 0.051 1236 Dihedral : 8.608 82.549 1088 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.97 % Favored : 91.92 % Rotamer: Outliers : 4.11 % Allowed : 12.84 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.30), residues: 916 helix: 1.56 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -2.71 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 108 TYR 0.010 0.001 TYR B 353 PHE 0.013 0.001 PHE A 35 TRP 0.010 0.001 TRP A 49 HIS 0.008 0.002 HIS A 556 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 7576) covalent geometry : angle 1.04138 (10336) hydrogen bonds : bond 0.04486 ( 446) hydrogen bonds : angle 4.06267 ( 1296) link_NAG-ASN : bond 0.00851 ( 2) link_NAG-ASN : angle 2.75343 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.7366 (mm) cc_final: 0.7152 (mt) REVERT: A 201 ARG cc_start: 0.6646 (mmm160) cc_final: 0.6146 (mmm160) REVERT: A 312 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6431 (tt) REVERT: A 391 PHE cc_start: 0.4896 (OUTLIER) cc_final: 0.4052 (m-80) REVERT: A 392 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.5418 (m-80) REVERT: B 115 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7921 (mt) REVERT: B 158 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6569 (mm-40) REVERT: B 312 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7343 (tt) REVERT: B 391 PHE cc_start: 0.4066 (OUTLIER) cc_final: 0.2900 (t80) REVERT: B 392 TYR cc_start: 0.3991 (OUTLIER) cc_final: 0.3169 (m-80) REVERT: B 413 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7499 (tt) REVERT: B 517 TYR cc_start: 0.8619 (m-80) cc_final: 0.8375 (m-80) outliers start: 33 outliers final: 24 residues processed: 134 average time/residue: 0.1573 time to fit residues: 30.4405 Evaluate side-chains 137 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 36 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 chunk 35 optimal weight: 0.5980 chunk 80 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.152677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.139844 restraints weight = 23262.082| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.56 r_work: 0.3629 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7578 Z= 0.136 Angle : 1.033 26.175 10342 Z= 0.450 Chirality : 0.182 1.730 1250 Planarity : 0.005 0.048 1236 Dihedral : 8.494 81.434 1088 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 4.24 % Allowed : 13.22 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.30), residues: 916 helix: 1.62 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -2.54 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 108 TYR 0.010 0.001 TYR B 353 PHE 0.011 0.001 PHE A 35 TRP 0.010 0.001 TRP B 49 HIS 0.009 0.002 HIS A 556 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7576) covalent geometry : angle 1.03101 (10336) hydrogen bonds : bond 0.04160 ( 446) hydrogen bonds : angle 3.98533 ( 1296) link_NAG-ASN : bond 0.00863 ( 2) link_NAG-ASN : angle 2.73996 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ARG cc_start: 0.6624 (mmm160) cc_final: 0.6144 (mmm160) REVERT: A 312 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6319 (tt) REVERT: A 391 PHE cc_start: 0.4884 (OUTLIER) cc_final: 0.4073 (m-80) REVERT: A 392 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.5490 (m-80) REVERT: B 115 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8003 (mt) REVERT: B 312 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7380 (tt) REVERT: B 391 PHE cc_start: 0.4005 (OUTLIER) cc_final: 0.2874 (t80) REVERT: B 392 TYR cc_start: 0.3987 (OUTLIER) cc_final: 0.3166 (m-80) REVERT: B 410 ILE cc_start: 0.8592 (tt) cc_final: 0.8384 (tp) REVERT: B 413 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7565 (tt) outliers start: 34 outliers final: 23 residues processed: 131 average time/residue: 0.1378 time to fit residues: 27.2172 Evaluate side-chains 135 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 48 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN B 465 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.148477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.135630 restraints weight = 23625.099| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.55 r_work: 0.3568 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7578 Z= 0.166 Angle : 1.046 26.301 10342 Z= 0.459 Chirality : 0.182 1.728 1250 Planarity : 0.006 0.048 1236 Dihedral : 8.256 79.811 1083 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 3.87 % Allowed : 13.47 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.30), residues: 916 helix: 1.55 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -2.55 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 307 TYR 0.009 0.001 TYR B 353 PHE 0.015 0.001 PHE A 35 TRP 0.011 0.001 TRP B 49 HIS 0.008 0.002 HIS A 556 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 7576) covalent geometry : angle 1.04404 (10336) hydrogen bonds : bond 0.04654 ( 446) hydrogen bonds : angle 4.02296 ( 1296) link_NAG-ASN : bond 0.00895 ( 2) link_NAG-ASN : angle 2.76797 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ARG cc_start: 0.6888 (mmm160) cc_final: 0.6343 (mmm160) REVERT: A 208 MET cc_start: 0.7105 (mmm) cc_final: 0.6887 (mmt) REVERT: A 304 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6374 (mp0) REVERT: A 312 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6271 (tt) REVERT: A 391 PHE cc_start: 0.4945 (OUTLIER) cc_final: 0.3974 (m-80) REVERT: A 392 TYR cc_start: 0.6890 (OUTLIER) cc_final: 0.5444 (m-80) REVERT: B 312 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7451 (tt) REVERT: B 391 PHE cc_start: 0.4089 (OUTLIER) cc_final: 0.3041 (t80) REVERT: B 392 TYR cc_start: 0.3880 (OUTLIER) cc_final: 0.3038 (m-80) REVERT: B 413 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7705 (tt) outliers start: 31 outliers final: 21 residues processed: 132 average time/residue: 0.1305 time to fit residues: 26.0379 Evaluate side-chains 132 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 559 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 0.0770 chunk 56 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.149135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136201 restraints weight = 23791.084| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.57 r_work: 0.3581 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7578 Z= 0.139 Angle : 1.032 26.167 10342 Z= 0.450 Chirality : 0.182 1.727 1250 Planarity : 0.005 0.045 1236 Dihedral : 8.060 78.079 1080 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.74 % Allowed : 13.72 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.30), residues: 916 helix: 1.60 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -2.55 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 108 TYR 0.009 0.001 TYR B 353 PHE 0.012 0.001 PHE B 35 TRP 0.011 0.001 TRP B 49 HIS 0.006 0.002 HIS A 556 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7576) covalent geometry : angle 1.03015 (10336) hydrogen bonds : bond 0.04274 ( 446) hydrogen bonds : angle 3.94158 ( 1296) link_NAG-ASN : bond 0.00864 ( 2) link_NAG-ASN : angle 2.73688 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ARG cc_start: 0.6836 (mmm160) cc_final: 0.6310 (mmm160) REVERT: A 312 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6335 (tt) REVERT: A 391 PHE cc_start: 0.4974 (OUTLIER) cc_final: 0.3943 (m-80) REVERT: A 392 TYR cc_start: 0.6889 (OUTLIER) cc_final: 0.5473 (m-80) REVERT: B 312 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7435 (tt) REVERT: B 391 PHE cc_start: 0.4108 (OUTLIER) cc_final: 0.3059 (t80) REVERT: B 392 TYR cc_start: 0.3792 (OUTLIER) cc_final: 0.2915 (m-80) REVERT: B 413 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7690 (tt) outliers start: 30 outliers final: 21 residues processed: 130 average time/residue: 0.1438 time to fit residues: 27.7975 Evaluate side-chains 131 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.146578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.133695 restraints weight = 23994.427| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.57 r_work: 0.3553 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7578 Z= 0.169 Angle : 1.043 26.232 10342 Z= 0.457 Chirality : 0.182 1.726 1250 Planarity : 0.005 0.046 1236 Dihedral : 8.068 77.158 1079 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 3.62 % Allowed : 13.84 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.30), residues: 916 helix: 1.53 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -2.53 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 108 TYR 0.009 0.001 TYR B 353 PHE 0.014 0.001 PHE A 35 TRP 0.012 0.001 TRP A 49 HIS 0.006 0.002 HIS A 556 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 7576) covalent geometry : angle 1.04090 (10336) hydrogen bonds : bond 0.04603 ( 446) hydrogen bonds : angle 3.97339 ( 1296) link_NAG-ASN : bond 0.00865 ( 2) link_NAG-ASN : angle 2.75265 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ARG cc_start: 0.6935 (mmm160) cc_final: 0.6389 (mmm160) REVERT: A 304 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6418 (mp0) REVERT: A 312 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6352 (tt) REVERT: A 391 PHE cc_start: 0.4937 (OUTLIER) cc_final: 0.3932 (m-80) REVERT: A 392 TYR cc_start: 0.6911 (OUTLIER) cc_final: 0.5493 (m-80) REVERT: B 312 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7438 (tt) REVERT: B 391 PHE cc_start: 0.4160 (OUTLIER) cc_final: 0.3124 (t80) REVERT: B 392 TYR cc_start: 0.3803 (OUTLIER) cc_final: 0.2943 (m-80) REVERT: B 413 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7741 (tt) outliers start: 29 outliers final: 21 residues processed: 129 average time/residue: 0.1448 time to fit residues: 28.2006 Evaluate side-chains 132 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 19 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 75 optimal weight: 0.0070 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.130578 restraints weight = 24330.592| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.58 r_work: 0.3555 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7578 Z= 0.156 Angle : 1.040 26.155 10342 Z= 0.455 Chirality : 0.182 1.728 1250 Planarity : 0.005 0.045 1236 Dihedral : 8.041 76.282 1079 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.24 % Allowed : 14.46 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.30), residues: 916 helix: 1.53 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -2.52 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 108 TYR 0.008 0.001 TYR B 353 PHE 0.013 0.001 PHE B 35 TRP 0.012 0.001 TRP A 49 HIS 0.006 0.002 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 7576) covalent geometry : angle 1.03826 (10336) hydrogen bonds : bond 0.04474 ( 446) hydrogen bonds : angle 3.96782 ( 1296) link_NAG-ASN : bond 0.00866 ( 2) link_NAG-ASN : angle 2.74405 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ARG cc_start: 0.6964 (mmm160) cc_final: 0.6417 (mmm160) REVERT: A 312 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6251 (tt) REVERT: A 391 PHE cc_start: 0.4936 (OUTLIER) cc_final: 0.3879 (m-80) REVERT: A 392 TYR cc_start: 0.6890 (OUTLIER) cc_final: 0.5491 (m-80) REVERT: B 48 TYR cc_start: 0.8509 (m-10) cc_final: 0.8237 (m-10) REVERT: B 312 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7432 (tt) REVERT: B 392 TYR cc_start: 0.3672 (OUTLIER) cc_final: 0.2867 (m-80) REVERT: B 413 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7745 (tt) outliers start: 26 outliers final: 19 residues processed: 131 average time/residue: 0.1365 time to fit residues: 26.7012 Evaluate side-chains 128 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 61 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.147575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.134812 restraints weight = 24010.557| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.54 r_work: 0.3552 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7578 Z= 0.144 Angle : 1.037 26.150 10342 Z= 0.453 Chirality : 0.182 1.725 1250 Planarity : 0.005 0.046 1236 Dihedral : 7.784 76.321 1075 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.37 % Allowed : 14.84 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.30), residues: 916 helix: 1.57 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -2.48 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 108 TYR 0.009 0.001 TYR B 353 PHE 0.012 0.001 PHE A 35 TRP 0.012 0.001 TRP A 49 HIS 0.006 0.002 HIS A 556 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 7576) covalent geometry : angle 1.03488 (10336) hydrogen bonds : bond 0.04344 ( 446) hydrogen bonds : angle 3.94422 ( 1296) link_NAG-ASN : bond 0.00871 ( 2) link_NAG-ASN : angle 2.73211 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3427.09 seconds wall clock time: 58 minutes 45.18 seconds (3525.18 seconds total)