Starting phenix.real_space_refine on Fri Jul 3 06:46:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eor_28465/07_2026/8eor_28465.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eor_28465/07_2026/8eor_28465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8eor_28465/07_2026/8eor_28465.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eor_28465/07_2026/8eor_28465.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eor_28465/07_2026/8eor_28465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eor_28465/07_2026/8eor_28465.map" model { file = "/net/cci-nas-00/data/ceres_data/8eor_28465/07_2026/8eor_28465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eor_28465/07_2026/8eor_28465.cif" } resolution = 2.67 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= 0.061 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 8064 2.51 5 N 2064 2.21 5 O 2334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12522 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4129 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 495} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4129 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 495} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 4129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4129 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 495} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'EEE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'EEE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'EEE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.65, per 1000 atoms: 0.21 Number of scatterers: 12522 At special positions: 0 Unit cell: (135, 128.52, 65.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2334 8.00 N 2064 7.00 C 8064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 285 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 285 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 274 " - pdb=" SG CYS C 285 " distance=2.03 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG E 1 " - " ASN B 79 " Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 453.8 milliseconds 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 9 sheets defined 43.2% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.530A pdb=" N THR A 151 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 188 through 205 Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 261 through 273 Processing helix chain 'A' and resid 278 through 288 Processing helix chain 'A' and resid 290 through 302 Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.951A pdb=" N GLU A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 371' Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 394 through 405 removed outlier: 4.584A pdb=" N GLU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 426 removed outlier: 3.635A pdb=" N ASP A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 440 Processing helix chain 'A' and resid 471 through 476 Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.607A pdb=" N LEU A 481 " --> pdb=" O GLY A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 507 Processing helix chain 'A' and resid 540 through 552 Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 90 through 102 Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.621A pdb=" N THR B 151 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 188 through 205 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 221 through 233 Processing helix chain 'B' and resid 261 through 273 Processing helix chain 'B' and resid 278 through 288 Processing helix chain 'B' and resid 290 through 302 Processing helix chain 'B' and resid 331 through 338 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 367 through 371 removed outlier: 4.055A pdb=" N GLU B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 371' Processing helix chain 'B' and resid 374 through 385 Processing helix chain 'B' and resid 394 through 405 removed outlier: 4.569A pdb=" N GLU B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 426 removed outlier: 3.810A pdb=" N ASP B 415 " --> pdb=" O VAL B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 440 Processing helix chain 'B' and resid 471 through 476 Processing helix chain 'B' and resid 477 through 482 removed outlier: 3.624A pdb=" N LEU B 481 " --> pdb=" O GLY B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 507 Processing helix chain 'B' and resid 540 through 552 Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 188 through 205 Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 261 through 273 Processing helix chain 'C' and resid 278 through 288 Processing helix chain 'C' and resid 290 through 302 Processing helix chain 'C' and resid 331 through 339 Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 367 through 371 removed outlier: 4.082A pdb=" N GLU C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 385 Processing helix chain 'C' and resid 394 through 405 removed outlier: 4.568A pdb=" N GLU C 398 " --> pdb=" O GLU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 426 removed outlier: 3.637A pdb=" N ASP C 415 " --> pdb=" O VAL C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 440 Processing helix chain 'C' and resid 471 through 476 Processing helix chain 'C' and resid 477 through 482 removed outlier: 3.586A pdb=" N LEU C 481 " --> pdb=" O GLY C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 507 Processing helix chain 'C' and resid 540 through 552 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.773A pdb=" N LYS A 32 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 38 removed outlier: 5.506A pdb=" N ILE A 49 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N THR A 123 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU A 51 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE A 121 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N LEU A 133 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N SER A 214 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 220 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ARG A 242 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL A 215 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ILE A 244 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 217 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLU A 246 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY A 219 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLY A 525 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N MET A 446 " --> pdb=" O GLY A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 removed outlier: 5.657A pdb=" N MET A 86 " --> pdb=" O SER A 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 25 through 27 removed outlier: 6.779A pdb=" N LYS B 32 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 36 through 38 removed outlier: 5.429A pdb=" N ILE B 49 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR B 123 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU B 51 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE B 121 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N LEU B 133 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N SER B 214 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU B 220 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ARG B 242 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 215 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ILE B 244 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE B 217 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLU B 246 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY B 219 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 447 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLY B 525 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N MET B 446 " --> pdb=" O GLY B 525 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 87 removed outlier: 5.673A pdb=" N MET B 86 " --> pdb=" O SER B 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.755A pdb=" N LYS C 32 " --> pdb=" O LYS C 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 36 through 38 removed outlier: 5.439A pdb=" N ILE C 49 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR C 123 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU C 51 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE C 121 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 9.838A pdb=" N LEU C 133 " --> pdb=" O PRO C 212 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER C 214 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 220 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 447 " --> pdb=" O VAL C 348 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLY C 525 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N MET C 446 " --> pdb=" O GLY C 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 87 removed outlier: 5.781A pdb=" N MET C 86 " --> pdb=" O SER C 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 552 hydrogen bonds defined for protein. 1584 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: 1.73 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2072 1.31 - 1.43: 3303 1.43 - 1.56: 7357 1.56 - 1.68: 0 1.68 - 1.81: 105 Bond restraints: 12837 Sorted by residual: bond pdb=" C TYR B 403 " pdb=" N LEU B 404 " ideal model delta sigma weight residual 1.333 1.418 -0.084 1.49e-02 4.50e+03 3.21e+01 bond pdb=" C TYR A 403 " pdb=" N LEU A 404 " ideal model delta sigma weight residual 1.333 1.403 -0.070 1.49e-02 4.50e+03 2.19e+01 bond pdb=" C ASN C 103 " pdb=" N ARG C 104 " ideal model delta sigma weight residual 1.330 1.267 0.063 1.37e-02 5.33e+03 2.09e+01 bond pdb=" C ASN A 103 " pdb=" N ARG A 104 " ideal model delta sigma weight residual 1.330 1.267 0.062 1.37e-02 5.33e+03 2.06e+01 bond pdb=" C ASN B 103 " pdb=" N ARG B 104 " ideal model delta sigma weight residual 1.330 1.268 0.061 1.37e-02 5.33e+03 2.01e+01 ... (remaining 12832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 16992 1.65 - 3.31: 308 3.31 - 4.96: 117 4.96 - 6.61: 13 6.61 - 8.26: 3 Bond angle restraints: 17433 Sorted by residual: angle pdb=" O TYR B 403 " pdb=" C TYR B 403 " pdb=" N LEU B 404 " ideal model delta sigma weight residual 122.30 127.53 -5.23 1.35e+00 5.49e-01 1.50e+01 angle pdb=" O TYR A 403 " pdb=" C TYR A 403 " pdb=" N LEU A 404 " ideal model delta sigma weight residual 122.32 126.77 -4.45 1.15e+00 7.56e-01 1.50e+01 angle pdb=" CA TYR B 403 " pdb=" C TYR B 403 " pdb=" N LEU B 404 " ideal model delta sigma weight residual 117.32 112.20 5.12 1.42e+00 4.96e-01 1.30e+01 angle pdb=" CA TYR A 403 " pdb=" C TYR A 403 " pdb=" N LEU A 404 " ideal model delta sigma weight residual 117.07 113.01 4.06 1.21e+00 6.83e-01 1.12e+01 angle pdb=" C2 EEE C 601 " pdb=" C1 EEE C 601 " pdb=" O2 EEE C 601 " ideal model delta sigma weight residual 111.51 119.77 -8.26 3.00e+00 1.11e-01 7.59e+00 ... (remaining 17428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 6949 14.30 - 28.61: 513 28.61 - 42.91: 114 42.91 - 57.22: 32 57.22 - 71.52: 6 Dihedral angle restraints: 7614 sinusoidal: 3051 harmonic: 4563 Sorted by residual: dihedral pdb=" CA PHE B 426 " pdb=" C PHE B 426 " pdb=" N GLY B 427 " pdb=" CA GLY B 427 " ideal model delta harmonic sigma weight residual -180.00 -162.19 -17.81 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASP B 203 " pdb=" C ASP B 203 " pdb=" N ASN B 204 " pdb=" CA ASN B 204 " ideal model delta harmonic sigma weight residual -180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP A 203 " pdb=" C ASP A 203 " pdb=" N ASN A 204 " pdb=" CA ASN A 204 " ideal model delta harmonic sigma weight residual 180.00 -162.93 -17.07 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 7611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1655 0.053 - 0.106: 236 0.106 - 0.158: 63 0.158 - 0.211: 0 0.211 - 0.264: 3 Chirality restraints: 1957 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1954 not shown) Planarity restraints: 2230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 404 " 0.010 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C LEU B 404 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU B 404 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY B 405 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 423 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C ASP A 423 " 0.029 2.00e-02 2.50e+03 pdb=" O ASP A 423 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 424 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 423 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C ASP B 423 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP B 423 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL B 424 " 0.010 2.00e-02 2.50e+03 ... (remaining 2227 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3665 2.82 - 3.34: 11445 3.34 - 3.86: 21321 3.86 - 4.38: 26618 4.38 - 4.90: 43489 Nonbonded interactions: 106538 Sorted by model distance: nonbonded pdb=" N GLU A 471 " pdb=" OE1 GLU A 471 " model vdw 2.303 3.120 nonbonded pdb=" OG SER C 247 " pdb=" OE2 GLU C 354 " model vdw 2.310 3.040 nonbonded pdb=" OG SER B 247 " pdb=" OE2 GLU B 354 " model vdw 2.328 3.040 nonbonded pdb=" N GLU C 471 " pdb=" OE1 GLU C 471 " model vdw 2.329 3.120 nonbonded pdb=" O HIS C 140 " pdb=" OH TYR C 170 " model vdw 2.339 3.040 ... (remaining 106533 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' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.310 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.190 Find NCS groups from input model: 0.220 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: 0.000 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 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 : 0.004 0.084 12850 Z= 0.208 Angle : 0.639 8.263 17466 Z= 0.345 Chirality : 0.042 0.264 1957 Planarity : 0.004 0.030 2229 Dihedral : 11.180 71.523 4668 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.45 % Allowed : 4.40 % Favored : 95.15 % 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: 0.50 (0.21), residues: 1590 helix: 1.42 (0.22), residues: 600 sheet: 0.72 (0.36), residues: 201 loop : -0.62 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 242 TYR 0.010 0.001 TYR C 152 PHE 0.010 0.001 PHE A 177 TRP 0.007 0.001 TRP B 74 HIS 0.002 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.21 (12837) covalent geometry : angle 0.63803 / 0.35 (17433) SS BOND : bond 0.00230 / 0.14 ( 6) SS BOND : angle 0.77016 / 0.59 ( 12) hydrogen bonds : bond 0.16382 / 11.04 ( 552) hydrogen bonds : angle 7.18455 / 5.25 ( 1584) link_BETA1-4 : bond 0.00424 / 0.24 ( 6) link_BETA1-4 : angle 1.31775 / 1.22 ( 18) link_NAG-ASN : bond 0.00244 / 0.13 ( 1) link_NAG-ASN : angle 1.22956 / 0.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 223 time to evaluate : 0.466 Fit side-chains REVERT: A 57 LYS cc_start: 0.8289 (tttt) cc_final: 0.8089 (tttt) REVERT: A 86 MET cc_start: 0.8385 (ptt) cc_final: 0.8076 (ptt) REVERT: A 106 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6771 (pm20) REVERT: A 111 LYS cc_start: 0.7609 (mtmm) cc_final: 0.7195 (mtmp) REVERT: A 132 ARG cc_start: 0.8240 (mmm160) cc_final: 0.8026 (mtt180) REVERT: A 199 ARG cc_start: 0.7445 (mtt-85) cc_final: 0.6721 (mtp180) REVERT: A 267 GLN cc_start: 0.6646 (tp40) cc_final: 0.6147 (mt0) REVERT: A 296 GLU cc_start: 0.7131 (tt0) cc_final: 0.6756 (tp30) REVERT: A 338 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7048 (mt-10) REVERT: A 376 LYS cc_start: 0.7045 (mttp) cc_final: 0.6774 (tppt) REVERT: A 379 MET cc_start: 0.7133 (mtp) cc_final: 0.6739 (mtt) REVERT: A 494 LYS cc_start: 0.7564 (mttt) cc_final: 0.7335 (mtmt) REVERT: B 95 GLN cc_start: 0.7462 (tt0) cc_final: 0.7125 (tt0) REVERT: B 106 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7134 (pm20) REVERT: B 111 LYS cc_start: 0.7766 (mtmm) cc_final: 0.7229 (mtmm) REVERT: B 132 ARG cc_start: 0.8048 (mmm160) cc_final: 0.7797 (mmt180) REVERT: B 199 ARG cc_start: 0.7111 (mtt-85) cc_final: 0.6507 (mtm110) REVERT: B 267 GLN cc_start: 0.6874 (tp40) cc_final: 0.6337 (mt0) REVERT: B 270 ILE cc_start: 0.7477 (mt) cc_final: 0.7194 (mm) REVERT: B 275 LYS cc_start: 0.7239 (mmtp) cc_final: 0.7009 (mtmt) REVERT: B 282 MET cc_start: 0.8066 (mtm) cc_final: 0.7801 (mtm) REVERT: B 296 GLU cc_start: 0.7070 (tt0) cc_final: 0.6580 (tp30) REVERT: B 338 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6919 (mt-10) REVERT: B 364 MET cc_start: 0.7194 (mtm) cc_final: 0.6759 (mtp) REVERT: B 494 LYS cc_start: 0.7388 (mttt) cc_final: 0.7056 (mtmt) REVERT: C 41 GLU cc_start: 0.7676 (tt0) cc_final: 0.7368 (mp0) REVERT: C 106 GLU cc_start: 0.7546 (mm-30) cc_final: 0.6759 (pm20) REVERT: C 111 LYS cc_start: 0.7632 (mtmm) cc_final: 0.7147 (mtmm) REVERT: C 132 ARG cc_start: 0.8196 (mmm160) cc_final: 0.7925 (mmt180) REVERT: C 199 ARG cc_start: 0.7138 (mtt-85) cc_final: 0.6393 (mtm110) REVERT: C 270 ILE cc_start: 0.7653 (mt) cc_final: 0.7373 (mm) REVERT: C 275 LYS cc_start: 0.7446 (mmtp) cc_final: 0.7197 (mtmt) REVERT: C 296 GLU cc_start: 0.6998 (tt0) cc_final: 0.6282 (tp30) REVERT: C 459 MET cc_start: 0.6999 (mmm) cc_final: 0.6665 (mtm) outliers start: 6 outliers final: 5 residues processed: 229 average time/residue: 0.6266 time to fit residues: 154.5594 Evaluate side-chains 165 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 160 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain C residue 218 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 GLN A 372 GLN B 340 ASN C 169 GLN C 372 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.136674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.113847 restraints weight = 12639.755| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.02 r_work: 0.3041 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12850 Z= 0.174 Angle : 0.613 7.894 17466 Z= 0.310 Chirality : 0.045 0.131 1957 Planarity : 0.005 0.041 2229 Dihedral : 4.645 29.361 1690 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.24 % Allowed : 10.74 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.44 (0.21), residues: 1590 helix: 1.39 (0.21), residues: 615 sheet: 0.33 (0.34), residues: 216 loop : -0.60 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 171 TYR 0.015 0.002 TYR B 152 PHE 0.018 0.002 PHE A 218 TRP 0.011 0.002 TRP C 74 HIS 0.004 0.001 HIS B 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.17 (12837) covalent geometry : angle 0.60994 / 0.31 (17433) SS BOND : bond 0.00256 / 0.14 ( 6) SS BOND : angle 1.91210 / 2.17 ( 12) hydrogen bonds : bond 0.04914 / 3.34 ( 552) hydrogen bonds : angle 5.69957 / 4.20 ( 1584) link_BETA1-4 : bond 0.00724 / 0.45 ( 6) link_BETA1-4 : angle 1.21083 / 1.39 ( 18) link_NAG-ASN : bond 0.00243 / 0.13 ( 1) link_NAG-ASN : angle 2.03593 / 1.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.491 Fit side-chains REVERT: A 86 MET cc_start: 0.8823 (ptt) cc_final: 0.8622 (ptt) REVERT: A 106 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7459 (pm20) REVERT: A 111 LYS cc_start: 0.8111 (mtmm) cc_final: 0.7901 (mtmp) REVERT: A 199 ARG cc_start: 0.8395 (mtt-85) cc_final: 0.8182 (mtp180) REVERT: A 267 GLN cc_start: 0.7769 (tp40) cc_final: 0.7379 (mt0) REVERT: A 296 GLU cc_start: 0.8145 (tt0) cc_final: 0.7705 (tp30) REVERT: A 379 MET cc_start: 0.7470 (mtp) cc_final: 0.7036 (mtt) REVERT: B 95 GLN cc_start: 0.8517 (tt0) cc_final: 0.8174 (tt0) REVERT: B 106 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7633 (pm20) REVERT: B 111 LYS cc_start: 0.8358 (mtmm) cc_final: 0.8103 (mtmm) REVERT: B 132 ARG cc_start: 0.8350 (mmm160) cc_final: 0.8056 (mmt180) REVERT: B 267 GLN cc_start: 0.7791 (tp40) cc_final: 0.7550 (mt0) REVERT: B 270 ILE cc_start: 0.8514 (mt) cc_final: 0.8292 (mm) REVERT: B 275 LYS cc_start: 0.7922 (mmtp) cc_final: 0.7666 (mtmt) REVERT: B 282 MET cc_start: 0.8949 (mtm) cc_final: 0.8720 (mtm) REVERT: B 296 GLU cc_start: 0.8116 (tt0) cc_final: 0.7853 (tp30) REVERT: B 338 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7334 (mt-10) REVERT: B 364 MET cc_start: 0.7547 (mtm) cc_final: 0.7228 (mtp) REVERT: B 421 ILE cc_start: 0.8616 (mm) cc_final: 0.8377 (mm) REVERT: B 487 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7270 (mm-30) REVERT: C 41 GLU cc_start: 0.8322 (tt0) cc_final: 0.7833 (mp0) REVERT: C 106 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7584 (pm20) REVERT: C 111 LYS cc_start: 0.8264 (mtmm) cc_final: 0.8020 (mtmm) REVERT: C 132 ARG cc_start: 0.8439 (mmm160) cc_final: 0.8137 (mmt180) REVERT: C 199 ARG cc_start: 0.8318 (mtt-85) cc_final: 0.8110 (mtm110) REVERT: C 296 GLU cc_start: 0.8145 (tt0) cc_final: 0.7633 (tp30) REVERT: C 459 MET cc_start: 0.7713 (mmm) cc_final: 0.7234 (mtm) outliers start: 30 outliers final: 17 residues processed: 165 average time/residue: 0.6764 time to fit residues: 120.2169 Evaluate side-chains 145 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 444 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 130 optimal weight: 0.8980 chunk 139 optimal weight: 0.0010 chunk 143 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 128 optimal weight: 5.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.139059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.115351 restraints weight = 12759.205| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.13 r_work: 0.3091 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12850 Z= 0.099 Angle : 0.507 5.421 17466 Z= 0.255 Chirality : 0.041 0.131 1957 Planarity : 0.004 0.044 2229 Dihedral : 4.308 28.134 1690 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.42 % Allowed : 13.12 % Favored : 85.46 % 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: 0.74 (0.21), residues: 1590 helix: 1.77 (0.21), residues: 615 sheet: 0.27 (0.33), residues: 216 loop : -0.49 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 171 TYR 0.008 0.001 TYR B 152 PHE 0.018 0.001 PHE A 218 TRP 0.011 0.001 TRP C 547 HIS 0.002 0.001 HIS B 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (12837) covalent geometry : angle 0.50400 / 0.25 (17433) SS BOND : bond 0.00301 / 0.15 ( 6) SS BOND : angle 1.68513 / 1.75 ( 12) hydrogen bonds : bond 0.03565 / 2.42 ( 552) hydrogen bonds : angle 5.31030 / 3.93 ( 1584) link_BETA1-4 : bond 0.00639 / 0.39 ( 6) link_BETA1-4 : angle 1.11771 / 1.27 ( 18) link_NAG-ASN : bond 0.00164 / 0.09 ( 1) link_NAG-ASN : angle 1.63341 / 0.95 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.348 Fit side-chains REVERT: A 106 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7537 (pm20) REVERT: A 111 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7838 (mtmp) REVERT: A 199 ARG cc_start: 0.8380 (mtt-85) cc_final: 0.8143 (mtp180) REVERT: A 296 GLU cc_start: 0.8152 (tt0) cc_final: 0.7663 (tp30) REVERT: A 379 MET cc_start: 0.7438 (mtp) cc_final: 0.7136 (mtt) REVERT: B 95 GLN cc_start: 0.8511 (tt0) cc_final: 0.8145 (tt0) REVERT: B 106 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7590 (pm20) REVERT: B 111 LYS cc_start: 0.8254 (mtmm) cc_final: 0.7910 (mtmt) REVERT: B 132 ARG cc_start: 0.8265 (mmm160) cc_final: 0.7989 (mmt180) REVERT: B 270 ILE cc_start: 0.8438 (mt) cc_final: 0.8236 (mm) REVERT: B 275 LYS cc_start: 0.7916 (mmtp) cc_final: 0.7686 (mtmt) REVERT: B 282 MET cc_start: 0.8905 (mtm) cc_final: 0.8637 (mtm) REVERT: B 296 GLU cc_start: 0.8111 (tt0) cc_final: 0.7805 (tp30) REVERT: B 326 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.7761 (mmt) REVERT: B 364 MET cc_start: 0.7571 (mtm) cc_final: 0.7298 (mtp) REVERT: C 41 GLU cc_start: 0.8418 (tt0) cc_final: 0.7812 (mp0) REVERT: C 106 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7585 (pm20) REVERT: C 111 LYS cc_start: 0.8196 (mtmm) cc_final: 0.7864 (mtmm) REVERT: C 132 ARG cc_start: 0.8414 (mmm160) cc_final: 0.8187 (mmt180) REVERT: C 199 ARG cc_start: 0.8279 (mtt-85) cc_final: 0.8066 (mtm110) REVERT: C 296 GLU cc_start: 0.8102 (tt0) cc_final: 0.7534 (tp30) REVERT: C 398 GLU cc_start: 0.6910 (tp30) cc_final: 0.6266 (tt0) REVERT: C 459 MET cc_start: 0.7666 (mmm) cc_final: 0.7173 (mtm) REVERT: C 471 GLU cc_start: 0.8441 (pm20) cc_final: 0.8186 (pm20) outliers start: 19 outliers final: 10 residues processed: 158 average time/residue: 0.6983 time to fit residues: 118.4903 Evaluate side-chains 140 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 363 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 13 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 68 optimal weight: 0.0970 chunk 146 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 267 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.135376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.110514 restraints weight = 12821.442| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.30 r_work: 0.3023 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12850 Z= 0.174 Angle : 0.597 7.440 17466 Z= 0.301 Chirality : 0.045 0.137 1957 Planarity : 0.004 0.045 2229 Dihedral : 4.528 27.648 1688 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.76 % Allowed : 12.23 % Favored : 85.01 % 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: 0.54 (0.20), residues: 1590 helix: 1.59 (0.21), residues: 612 sheet: 0.24 (0.33), residues: 216 loop : -0.60 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 104 TYR 0.015 0.002 TYR B 152 PHE 0.017 0.002 PHE A 218 TRP 0.010 0.002 TRP B 74 HIS 0.005 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.17 (12837) covalent geometry : angle 0.59033 / 0.30 (17433) SS BOND : bond 0.00276 / 0.15 ( 6) SS BOND : angle 2.96610 / 2.13 ( 12) hydrogen bonds : bond 0.04414 / 3.00 ( 552) hydrogen bonds : angle 5.39757 / 3.99 ( 1584) link_BETA1-4 : bond 0.00697 / 0.41 ( 6) link_BETA1-4 : angle 1.23483 / 1.35 ( 18) link_NAG-ASN : bond 0.00273 / 0.14 ( 1) link_NAG-ASN : angle 2.02189 / 1.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.412 Fit side-chains REVERT: A 106 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7401 (pm20) REVERT: A 111 LYS cc_start: 0.8227 (mtmm) cc_final: 0.7892 (mtmp) REVERT: A 199 ARG cc_start: 0.8412 (mtt-85) cc_final: 0.8154 (mtp180) REVERT: A 296 GLU cc_start: 0.8162 (tt0) cc_final: 0.7651 (tp30) REVERT: A 376 LYS cc_start: 0.7449 (mttp) cc_final: 0.6969 (tppt) REVERT: A 379 MET cc_start: 0.7441 (mtp) cc_final: 0.7239 (mtt) REVERT: B 95 GLN cc_start: 0.8483 (tt0) cc_final: 0.8121 (tt0) REVERT: B 106 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7562 (pm20) REVERT: B 111 LYS cc_start: 0.8334 (mtmm) cc_final: 0.7928 (mtmt) REVERT: B 132 ARG cc_start: 0.8315 (mmm160) cc_final: 0.8004 (mmt180) REVERT: B 270 ILE cc_start: 0.8505 (mt) cc_final: 0.8263 (mm) REVERT: B 275 LYS cc_start: 0.8051 (mmtp) cc_final: 0.7764 (mtmt) REVERT: B 282 MET cc_start: 0.8908 (mtm) cc_final: 0.8628 (mtm) REVERT: B 296 GLU cc_start: 0.8175 (tt0) cc_final: 0.7796 (tp30) REVERT: B 326 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8174 (mmt) REVERT: B 363 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5775 (mp) REVERT: B 364 MET cc_start: 0.7612 (mtm) cc_final: 0.7340 (mtp) REVERT: B 457 SER cc_start: 0.8426 (OUTLIER) cc_final: 0.8125 (p) REVERT: B 487 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7339 (mm-30) REVERT: C 41 GLU cc_start: 0.8386 (tt0) cc_final: 0.7863 (mp0) REVERT: C 106 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7520 (pm20) REVERT: C 111 LYS cc_start: 0.8241 (mtmm) cc_final: 0.7959 (mtmm) REVERT: C 132 ARG cc_start: 0.8476 (mmm160) cc_final: 0.8235 (mmt180) REVERT: C 199 ARG cc_start: 0.8332 (mtt-85) cc_final: 0.8029 (mtm110) REVERT: C 296 GLU cc_start: 0.8131 (tt0) cc_final: 0.7548 (tp30) REVERT: C 459 MET cc_start: 0.7772 (mmm) cc_final: 0.7262 (mtm) outliers start: 37 outliers final: 16 residues processed: 162 average time/residue: 0.6080 time to fit residues: 106.3352 Evaluate side-chains 145 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 532 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 51 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 135 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 267 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.139063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.113274 restraints weight = 12676.642| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.45 r_work: 0.3058 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12850 Z= 0.116 Angle : 0.534 5.737 17466 Z= 0.269 Chirality : 0.042 0.154 1957 Planarity : 0.004 0.045 2229 Dihedral : 4.432 28.551 1688 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.24 % Allowed : 13.20 % Favored : 84.56 % 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: 0.66 (0.21), residues: 1590 helix: 1.75 (0.21), residues: 612 sheet: 0.23 (0.33), residues: 216 loop : -0.58 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 104 TYR 0.010 0.001 TYR B 152 PHE 0.016 0.001 PHE A 218 TRP 0.009 0.001 TRP B 547 HIS 0.003 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (12837) covalent geometry : angle 0.52816 / 0.27 (17433) SS BOND : bond 0.00204 / 0.11 ( 6) SS BOND : angle 2.67133 / 3.08 ( 12) hydrogen bonds : bond 0.03667 / 2.49 ( 552) hydrogen bonds : angle 5.23778 / 3.88 ( 1584) link_BETA1-4 : bond 0.00652 / 0.39 ( 6) link_BETA1-4 : angle 1.16384 / 1.30 ( 18) link_NAG-ASN : bond 0.00181 / 0.10 ( 1) link_NAG-ASN : angle 1.84301 / 1.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.491 Fit side-chains REVERT: A 106 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7388 (pm20) REVERT: A 111 LYS cc_start: 0.8184 (mtmm) cc_final: 0.7862 (mtmp) REVERT: A 199 ARG cc_start: 0.8413 (mtt-85) cc_final: 0.8171 (mtp180) REVERT: A 296 GLU cc_start: 0.8154 (tt0) cc_final: 0.7650 (tp30) REVERT: A 326 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8068 (mmt) REVERT: A 376 LYS cc_start: 0.7463 (mttp) cc_final: 0.6980 (tppt) REVERT: A 379 MET cc_start: 0.7454 (mtp) cc_final: 0.7209 (mtt) REVERT: B 92 LYS cc_start: 0.8396 (mttp) cc_final: 0.7847 (mtmm) REVERT: B 95 GLN cc_start: 0.8479 (tt0) cc_final: 0.8020 (tt0) REVERT: B 106 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7550 (pm20) REVERT: B 111 LYS cc_start: 0.8305 (mtmm) cc_final: 0.7909 (mtmt) REVERT: B 132 ARG cc_start: 0.8286 (mmm160) cc_final: 0.7991 (mmt180) REVERT: B 270 ILE cc_start: 0.8463 (mt) cc_final: 0.8241 (mm) REVERT: B 275 LYS cc_start: 0.7411 (mmtp) cc_final: 0.7134 (mtmt) REVERT: B 282 MET cc_start: 0.8866 (mtm) cc_final: 0.8619 (mtm) REVERT: B 296 GLU cc_start: 0.8154 (tt0) cc_final: 0.7916 (tp30) REVERT: B 363 LEU cc_start: 0.5786 (OUTLIER) cc_final: 0.5481 (mp) REVERT: B 364 MET cc_start: 0.7579 (mtm) cc_final: 0.7343 (mtp) REVERT: B 457 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.8164 (p) REVERT: B 487 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7296 (mm-30) REVERT: C 41 GLU cc_start: 0.8472 (tt0) cc_final: 0.7941 (mp0) REVERT: C 106 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7473 (pm20) REVERT: C 111 LYS cc_start: 0.8227 (mtmm) cc_final: 0.7957 (mtmm) REVERT: C 132 ARG cc_start: 0.8468 (mmm160) cc_final: 0.8235 (mmt180) REVERT: C 199 ARG cc_start: 0.8314 (mtt-85) cc_final: 0.8087 (mtm110) REVERT: C 296 GLU cc_start: 0.8128 (tt0) cc_final: 0.7535 (tp30) REVERT: C 398 GLU cc_start: 0.6941 (tp30) cc_final: 0.6307 (tt0) REVERT: C 459 MET cc_start: 0.7751 (mmm) cc_final: 0.7269 (mtm) outliers start: 30 outliers final: 15 residues processed: 158 average time/residue: 0.6627 time to fit residues: 113.1823 Evaluate side-chains 146 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 363 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 115 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 144 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 267 GLN B 340 ASN C 69 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.137605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.112188 restraints weight = 12656.302| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.37 r_work: 0.3039 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12850 Z= 0.151 Angle : 0.572 6.564 17466 Z= 0.288 Chirality : 0.044 0.140 1957 Planarity : 0.004 0.046 2229 Dihedral : 4.567 27.767 1688 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.61 % Allowed : 13.72 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.56 (0.21), residues: 1590 helix: 1.64 (0.21), residues: 612 sheet: 0.24 (0.33), residues: 216 loop : -0.62 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 171 TYR 0.014 0.002 TYR B 152 PHE 0.019 0.002 PHE A 218 TRP 0.010 0.002 TRP B 74 HIS 0.004 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.15 (12837) covalent geometry : angle 0.56797 / 0.29 (17433) SS BOND : bond 0.00234 / 0.12 ( 6) SS BOND : angle 2.17508 / 1.91 ( 12) hydrogen bonds : bond 0.04056 / 2.76 ( 552) hydrogen bonds : angle 5.29314 / 3.92 ( 1584) link_BETA1-4 : bond 0.00674 / 0.40 ( 6) link_BETA1-4 : angle 1.21728 / 1.33 ( 18) link_NAG-ASN : bond 0.00216 / 0.11 ( 1) link_NAG-ASN : angle 1.96701 / 1.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.552 Fit side-chains REVERT: A 106 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7414 (pm20) REVERT: A 111 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7894 (mtmp) REVERT: A 326 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8113 (mmt) REVERT: A 376 LYS cc_start: 0.7444 (mttp) cc_final: 0.6962 (tppt) REVERT: A 379 MET cc_start: 0.7500 (mtp) cc_final: 0.7235 (mtt) REVERT: B 92 LYS cc_start: 0.8393 (mttp) cc_final: 0.7846 (mtmm) REVERT: B 95 GLN cc_start: 0.8467 (tt0) cc_final: 0.8124 (tt0) REVERT: B 106 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7574 (pm20) REVERT: B 111 LYS cc_start: 0.8305 (mtmm) cc_final: 0.7926 (mtmt) REVERT: B 132 ARG cc_start: 0.8309 (mmm160) cc_final: 0.8015 (mmt180) REVERT: B 270 ILE cc_start: 0.8520 (mt) cc_final: 0.8295 (mm) REVERT: B 275 LYS cc_start: 0.7604 (mmtp) cc_final: 0.7224 (mtmt) REVERT: B 282 MET cc_start: 0.8913 (mtm) cc_final: 0.8674 (mtm) REVERT: B 296 GLU cc_start: 0.8172 (tt0) cc_final: 0.7804 (tp30) REVERT: B 363 LEU cc_start: 0.5717 (OUTLIER) cc_final: 0.5387 (mp) REVERT: B 364 MET cc_start: 0.7598 (mtm) cc_final: 0.7317 (mtp) REVERT: B 457 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.8233 (p) REVERT: B 487 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7227 (mm-30) REVERT: C 41 GLU cc_start: 0.8450 (tt0) cc_final: 0.7947 (mp0) REVERT: C 106 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7521 (pm20) REVERT: C 111 LYS cc_start: 0.8264 (mtmm) cc_final: 0.8000 (mtmm) REVERT: C 132 ARG cc_start: 0.8487 (mmm160) cc_final: 0.8253 (mmt180) REVERT: C 199 ARG cc_start: 0.8328 (mtt-85) cc_final: 0.8106 (mtm110) REVERT: C 296 GLU cc_start: 0.8139 (tt0) cc_final: 0.7556 (tp30) REVERT: C 459 MET cc_start: 0.7768 (mmm) cc_final: 0.7284 (mtm) outliers start: 35 outliers final: 18 residues processed: 160 average time/residue: 0.6679 time to fit residues: 115.4200 Evaluate side-chains 148 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 532 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 32 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 56 optimal weight: 0.0770 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 25 optimal weight: 0.0000 chunk 149 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 overall best weight: 0.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 GLN B 267 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.138831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.114008 restraints weight = 12601.232| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.33 r_work: 0.3081 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12850 Z= 0.117 Angle : 0.539 5.699 17466 Z= 0.270 Chirality : 0.042 0.128 1957 Planarity : 0.004 0.046 2229 Dihedral : 4.439 28.237 1688 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.46 % Allowed : 14.17 % Favored : 83.37 % 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: 0.65 (0.21), residues: 1590 helix: 1.75 (0.21), residues: 612 sheet: 0.26 (0.33), residues: 216 loop : -0.60 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 199 TYR 0.010 0.001 TYR B 152 PHE 0.018 0.001 PHE A 218 TRP 0.009 0.001 TRP B 547 HIS 0.004 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (12837) covalent geometry : angle 0.53213 / 0.27 (17433) SS BOND : bond 0.00220 / 0.11 ( 6) SS BOND : angle 2.82887 / 2.98 ( 12) hydrogen bonds : bond 0.03625 / 2.46 ( 552) hydrogen bonds : angle 5.18848 / 3.85 ( 1584) link_BETA1-4 : bond 0.00565 / 0.35 ( 6) link_BETA1-4 : angle 1.22316 / 1.44 ( 18) link_NAG-ASN : bond 0.00181 / 0.10 ( 1) link_NAG-ASN : angle 1.86148 / 1.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.507 Fit side-chains REVERT: A 106 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7363 (pm20) REVERT: A 111 LYS cc_start: 0.8185 (mtmm) cc_final: 0.7871 (mtmp) REVERT: A 376 LYS cc_start: 0.7434 (mttp) cc_final: 0.6925 (tppt) REVERT: A 379 MET cc_start: 0.7447 (mtp) cc_final: 0.7150 (mtt) REVERT: B 69 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8020 (mt0) REVERT: B 92 LYS cc_start: 0.8387 (mttp) cc_final: 0.7839 (mtmm) REVERT: B 95 GLN cc_start: 0.8484 (tt0) cc_final: 0.8146 (tt0) REVERT: B 106 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7569 (pm20) REVERT: B 111 LYS cc_start: 0.8250 (mtmm) cc_final: 0.7896 (mtmt) REVERT: B 132 ARG cc_start: 0.8313 (mmm160) cc_final: 0.8036 (mmt180) REVERT: B 270 ILE cc_start: 0.8503 (mt) cc_final: 0.8293 (mm) REVERT: B 275 LYS cc_start: 0.7446 (mmtp) cc_final: 0.7146 (mtmt) REVERT: B 282 MET cc_start: 0.8902 (mtm) cc_final: 0.8657 (mtm) REVERT: B 296 GLU cc_start: 0.8153 (tt0) cc_final: 0.7909 (tp30) REVERT: B 326 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.7467 (mmp) REVERT: B 363 LEU cc_start: 0.5728 (OUTLIER) cc_final: 0.5380 (mp) REVERT: B 364 MET cc_start: 0.7562 (mtm) cc_final: 0.7329 (mtp) REVERT: B 457 SER cc_start: 0.8518 (OUTLIER) cc_final: 0.8240 (p) REVERT: B 487 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7173 (mm-30) REVERT: C 41 GLU cc_start: 0.8474 (tt0) cc_final: 0.7921 (mp0) REVERT: C 106 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7467 (pm20) REVERT: C 111 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7957 (mtmm) REVERT: C 132 ARG cc_start: 0.8441 (mmm160) cc_final: 0.8204 (mmt180) REVERT: C 199 ARG cc_start: 0.8350 (mtt-85) cc_final: 0.8116 (mtm110) REVERT: C 296 GLU cc_start: 0.8153 (tt0) cc_final: 0.7546 (tp30) REVERT: C 398 GLU cc_start: 0.6991 (tp30) cc_final: 0.6319 (tt0) REVERT: C 459 MET cc_start: 0.7759 (mmm) cc_final: 0.7279 (mtm) outliers start: 33 outliers final: 19 residues processed: 155 average time/residue: 0.6275 time to fit residues: 105.2100 Evaluate side-chains 151 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 444 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 120 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN C 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.135535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.109916 restraints weight = 12623.660| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.44 r_work: 0.3023 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 12850 Z= 0.236 Angle : 0.682 10.459 17466 Z= 0.345 Chirality : 0.048 0.168 1957 Planarity : 0.005 0.047 2229 Dihedral : 4.838 27.639 1688 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.91 % Allowed : 13.94 % Favored : 83.15 % 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: 0.26 (0.20), residues: 1590 helix: 1.29 (0.21), residues: 612 sheet: 0.22 (0.33), residues: 216 loop : -0.75 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 171 TYR 0.016 0.002 TYR B 152 PHE 0.018 0.002 PHE A 218 TRP 0.012 0.002 TRP B 74 HIS 0.006 0.002 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.24 (12837) covalent geometry : angle 0.67164 / 0.34 (17433) SS BOND : bond 0.00477 / 0.25 ( 6) SS BOND : angle 4.20707 / 4.98 ( 12) hydrogen bonds : bond 0.04890 / 3.32 ( 552) hydrogen bonds : angle 5.44870 / 4.03 ( 1584) link_BETA1-4 : bond 0.00705 / 0.42 ( 6) link_BETA1-4 : angle 1.31067 / 1.43 ( 18) link_NAG-ASN : bond 0.00215 / 0.11 ( 1) link_NAG-ASN : angle 2.41196 / 1.35 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.364 Fit side-chains REVERT: A 106 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7465 (pm20) REVERT: A 111 LYS cc_start: 0.8189 (mtmm) cc_final: 0.7874 (mtmp) REVERT: A 376 LYS cc_start: 0.7494 (mttp) cc_final: 0.7006 (tppt) REVERT: A 379 MET cc_start: 0.7451 (mtp) cc_final: 0.7207 (mtt) REVERT: B 69 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8041 (mt0) REVERT: B 95 GLN cc_start: 0.8506 (tt0) cc_final: 0.8168 (tt0) REVERT: B 106 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7592 (pm20) REVERT: B 111 LYS cc_start: 0.8287 (mtmm) cc_final: 0.7941 (mtmm) REVERT: B 132 ARG cc_start: 0.8382 (mmm160) cc_final: 0.8077 (mmt180) REVERT: B 270 ILE cc_start: 0.8535 (mt) cc_final: 0.8282 (mm) REVERT: B 275 LYS cc_start: 0.7687 (mmtp) cc_final: 0.7281 (mtmt) REVERT: B 282 MET cc_start: 0.8934 (mtm) cc_final: 0.8698 (mtm) REVERT: B 296 GLU cc_start: 0.8242 (tt0) cc_final: 0.7852 (tp30) REVERT: B 326 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.7860 (mmp) REVERT: B 363 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5397 (mp) REVERT: B 364 MET cc_start: 0.7585 (mtm) cc_final: 0.7329 (mtp) REVERT: B 421 ILE cc_start: 0.8585 (mm) cc_final: 0.8341 (mm) REVERT: B 457 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8265 (p) REVERT: B 487 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7282 (mm-30) REVERT: C 41 GLU cc_start: 0.8445 (tt0) cc_final: 0.7976 (mp0) REVERT: C 106 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7520 (pm20) REVERT: C 111 LYS cc_start: 0.8316 (mtmm) cc_final: 0.8070 (mtmm) REVERT: C 132 ARG cc_start: 0.8487 (mmm160) cc_final: 0.8240 (mmt180) REVERT: C 199 ARG cc_start: 0.8355 (mtt-85) cc_final: 0.8076 (mtm110) REVERT: C 296 GLU cc_start: 0.8219 (tt0) cc_final: 0.7637 (tp30) REVERT: C 459 MET cc_start: 0.7753 (mmm) cc_final: 0.7249 (mtm) outliers start: 39 outliers final: 24 residues processed: 160 average time/residue: 0.5938 time to fit residues: 102.6655 Evaluate side-chains 159 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 532 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 37 optimal weight: 0.0270 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN C 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.138542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.113028 restraints weight = 12596.739| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.50 r_work: 0.3066 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12850 Z= 0.121 Angle : 0.556 8.135 17466 Z= 0.281 Chirality : 0.042 0.126 1957 Planarity : 0.004 0.045 2229 Dihedral : 4.549 28.117 1688 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.09 % Allowed : 14.99 % Favored : 82.92 % 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: 0.49 (0.21), residues: 1590 helix: 1.59 (0.21), residues: 612 sheet: 0.23 (0.33), residues: 216 loop : -0.68 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 199 TYR 0.010 0.001 TYR C 152 PHE 0.018 0.001 PHE A 218 TRP 0.010 0.002 TRP C 74 HIS 0.004 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (12837) covalent geometry : angle 0.54602 / 0.28 (17433) SS BOND : bond 0.00354 / 0.18 ( 6) SS BOND : angle 3.74934 / 4.14 ( 12) hydrogen bonds : bond 0.03692 / 2.51 ( 552) hydrogen bonds : angle 5.19924 / 3.86 ( 1584) link_BETA1-4 : bond 0.00611 / 0.37 ( 6) link_BETA1-4 : angle 1.20718 / 1.29 ( 18) link_NAG-ASN : bond 0.00186 / 0.10 ( 1) link_NAG-ASN : angle 2.08093 / 1.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.334 Fit side-chains REVERT: A 106 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7356 (pm20) REVERT: A 111 LYS cc_start: 0.8151 (mtmm) cc_final: 0.7853 (mtmp) REVERT: A 376 LYS cc_start: 0.7390 (mttp) cc_final: 0.6889 (tppt) REVERT: A 379 MET cc_start: 0.7457 (mtp) cc_final: 0.7166 (mtt) REVERT: B 69 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: B 95 GLN cc_start: 0.8505 (tt0) cc_final: 0.8172 (tt0) REVERT: B 106 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7586 (pm20) REVERT: B 111 LYS cc_start: 0.8272 (mtmm) cc_final: 0.7915 (mtmt) REVERT: B 132 ARG cc_start: 0.8341 (mmm160) cc_final: 0.8068 (mmt180) REVERT: B 270 ILE cc_start: 0.8523 (mt) cc_final: 0.8307 (mm) REVERT: B 275 LYS cc_start: 0.7419 (mmtp) cc_final: 0.7082 (mtmt) REVERT: B 282 MET cc_start: 0.8931 (mtm) cc_final: 0.8691 (mtm) REVERT: B 296 GLU cc_start: 0.8199 (tt0) cc_final: 0.7845 (tp30) REVERT: B 363 LEU cc_start: 0.5640 (OUTLIER) cc_final: 0.5274 (mp) REVERT: B 364 MET cc_start: 0.7560 (mtm) cc_final: 0.7320 (mtp) REVERT: B 457 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8256 (p) REVERT: B 487 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7229 (mm-30) REVERT: C 41 GLU cc_start: 0.8460 (tt0) cc_final: 0.7982 (mp0) REVERT: C 106 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7450 (pm20) REVERT: C 111 LYS cc_start: 0.8279 (mtmm) cc_final: 0.8040 (mtmm) REVERT: C 132 ARG cc_start: 0.8437 (mmm160) cc_final: 0.8200 (mmt180) REVERT: C 199 ARG cc_start: 0.8380 (mtt-85) cc_final: 0.8143 (mtm110) REVERT: C 285 CYS cc_start: 0.7462 (m) cc_final: 0.7141 (t) REVERT: C 296 GLU cc_start: 0.8190 (tt0) cc_final: 0.7582 (tp30) REVERT: C 398 GLU cc_start: 0.7025 (tp30) cc_final: 0.6343 (tt0) REVERT: C 459 MET cc_start: 0.7799 (mmm) cc_final: 0.7352 (mtm) REVERT: C 487 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7788 (tp30) outliers start: 28 outliers final: 16 residues processed: 156 average time/residue: 0.6415 time to fit residues: 107.8730 Evaluate side-chains 148 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 135 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN C 69 GLN C 267 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.136327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.111759 restraints weight = 12757.402| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.20 r_work: 0.3062 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12850 Z= 0.176 Angle : 0.616 8.311 17466 Z= 0.311 Chirality : 0.045 0.133 1957 Planarity : 0.005 0.046 2229 Dihedral : 4.680 27.366 1688 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.94 % Allowed : 15.21 % Favored : 82.85 % 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: 0.36 (0.20), residues: 1590 helix: 1.43 (0.21), residues: 612 sheet: 0.22 (0.33), residues: 216 loop : -0.72 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 199 TYR 0.015 0.002 TYR B 152 PHE 0.018 0.002 PHE A 218 TRP 0.010 0.002 TRP B 74 HIS 0.005 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 (12837) covalent geometry : angle 0.60513 / 0.31 (17433) SS BOND : bond 0.00341 / 0.18 ( 6) SS BOND : angle 4.08101 / 4.38 ( 12) hydrogen bonds : bond 0.04320 / 2.94 ( 552) hydrogen bonds : angle 5.32423 / 3.94 ( 1584) link_BETA1-4 : bond 0.00640 / 0.39 ( 6) link_BETA1-4 : angle 1.31322 / 1.39 ( 18) link_NAG-ASN : bond 0.00230 / 0.12 ( 1) link_NAG-ASN : angle 2.20956 / 1.25 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.572 Fit side-chains REVERT: A 106 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7446 (pm20) REVERT: A 111 LYS cc_start: 0.8165 (mtmm) cc_final: 0.7876 (mtmp) REVERT: A 376 LYS cc_start: 0.7502 (mttp) cc_final: 0.7020 (tppt) REVERT: A 379 MET cc_start: 0.7469 (mtp) cc_final: 0.7199 (mtt) REVERT: A 459 MET cc_start: 0.8141 (mpp) cc_final: 0.7843 (mtt) REVERT: B 69 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8009 (mt0) REVERT: B 95 GLN cc_start: 0.8483 (tt0) cc_final: 0.8146 (tt0) REVERT: B 106 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7596 (pm20) REVERT: B 111 LYS cc_start: 0.8279 (mtmm) cc_final: 0.7920 (mtmt) REVERT: B 132 ARG cc_start: 0.8353 (mmm160) cc_final: 0.8072 (mmt180) REVERT: B 270 ILE cc_start: 0.8531 (mt) cc_final: 0.8297 (mm) REVERT: B 282 MET cc_start: 0.8910 (mtm) cc_final: 0.8669 (mtm) REVERT: B 296 GLU cc_start: 0.8197 (tt0) cc_final: 0.7809 (tp30) REVERT: B 326 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.7474 (mmp) REVERT: B 363 LEU cc_start: 0.5645 (OUTLIER) cc_final: 0.5271 (mp) REVERT: B 364 MET cc_start: 0.7574 (mtm) cc_final: 0.7346 (mtp) REVERT: B 457 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8274 (p) REVERT: B 487 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7231 (mm-30) REVERT: B 521 ASN cc_start: 0.8191 (p0) cc_final: 0.7919 (p0) REVERT: C 41 GLU cc_start: 0.8399 (tt0) cc_final: 0.7976 (mp0) REVERT: C 106 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7512 (pm20) REVERT: C 111 LYS cc_start: 0.8292 (mtmm) cc_final: 0.8063 (mtmm) REVERT: C 132 ARG cc_start: 0.8449 (mmm160) cc_final: 0.8208 (mmt180) REVERT: C 199 ARG cc_start: 0.8344 (mtt-85) cc_final: 0.8121 (mtm110) REVERT: C 296 GLU cc_start: 0.8153 (tt0) cc_final: 0.7572 (tp30) REVERT: C 459 MET cc_start: 0.7789 (mmm) cc_final: 0.7377 (mtm) outliers start: 26 outliers final: 18 residues processed: 147 average time/residue: 0.7031 time to fit residues: 111.2612 Evaluate side-chains 149 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 85 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 5 optimal weight: 0.0770 chunk 15 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 12 optimal weight: 0.0670 chunk 107 optimal weight: 1.9990 chunk 93 optimal weight: 0.2980 chunk 133 optimal weight: 2.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.135923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.111002 restraints weight = 12796.898| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.23 r_work: 0.3034 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 12850 Z= 0.173 Angle : 0.855 59.199 17466 Z= 0.489 Chirality : 0.043 0.252 1957 Planarity : 0.005 0.046 2229 Dihedral : 4.707 27.380 1688 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.09 % Allowed : 15.14 % Favored : 82.77 % Cbeta Deviations : 0.07 % 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: 0.37 (0.20), residues: 1590 helix: 1.46 (0.21), residues: 612 sheet: 0.22 (0.32), residues: 216 loop : -0.74 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 199 TYR 0.013 0.001 TYR B 152 PHE 0.019 0.001 PHE A 218 TRP 0.010 0.001 TRP B 74 HIS 0.004 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (12837) covalent geometry : angle 0.84733 / 0.49 (17433) SS BOND : bond 0.00079 / 0.04 ( 6) SS BOND : angle 4.13085 / 5.01 ( 12) hydrogen bonds : bond 0.04170 / 2.83 ( 552) hydrogen bonds : angle 5.31990 / 3.94 ( 1584) link_BETA1-4 : bond 0.00597 / 0.37 ( 6) link_BETA1-4 : angle 1.31608 / 1.39 ( 18) link_NAG-ASN : bond 0.00281 / 0.15 ( 1) link_NAG-ASN : angle 2.22941 / 1.27 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3959.82 seconds wall clock time: 68 minutes 18.05 seconds (4098.05 seconds total)