Starting phenix.real_space_refine on Sat Aug 23 14:27:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eor_28465/08_2025/8eor_28465.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eor_28465/08_2025/8eor_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8eor_28465/08_2025/8eor_28465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eor_28465/08_2025/8eor_28465.map" model { file = "/net/cci-nas-00/data/ceres_data/8eor_28465/08_2025/8eor_28465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eor_28465/08_2025/8eor_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-2.0-5787/lib/python3.9/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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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: 3.07, per 1000 atoms: 0.25 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: 1.14 Conformation dependent library (CDL) restraints added in 545.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.48 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: 1.82 Time building geometry restraints manager: 1.44 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 - 21.65: 7448 21.65 - 43.29: 282 43.29 - 64.94: 40 64.94 - 86.59: 21 86.59 - 108.24: 12 Dihedral angle restraints: 7803 sinusoidal: 3240 harmonic: 4563 Sorted by residual: dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.53 108.24 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.03 107.74 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" O4 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.19 106.90 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 7800 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: 0.03 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: 1.780 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.290 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 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 : 13.327 108.235 4857 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 aren 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 covalent geometry : bond 0.00390 (12837) covalent geometry : angle 0.63803 (17433) SS BOND : bond 0.00230 ( 6) SS BOND : angle 0.77016 ( 12) hydrogen bonds : bond 0.16382 ( 552) hydrogen bonds : angle 7.18455 ( 1584) link_BETA1-4 : bond 0.00424 ( 6) link_BETA1-4 : angle 1.31775 ( 18) link_NAG-ASN : bond 0.00244 ( 1) link_NAG-ASN : angle 1.22956 ( 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 : 0.436 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: 0.7194 (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: 0.6727 time to fit residues: 165.5934 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 : 0.504 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3475 r_free = 0.3475 target = 0.136414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.113644 restraints weight = 12648.449| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.02 r_work: 0.3065 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12850 Z= 0.173 Angle : 0.614 7.972 17466 Z= 0.309 Chirality : 0.045 0.134 1957 Planarity : 0.005 0.042 2229 Dihedral : 9.325 70.886 1879 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.09 % Allowed : 10.66 % Favored : 87.25 % 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 aren not related in a simple way. whole: 0.43 (0.21), residues: 1590 helix: 1.38 (0.21), residues: 615 sheet: 0.30 (0.34), residues: 216 loop : -0.61 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 171 TYR 0.016 0.002 TYR C 152 PHE 0.018 0.002 PHE A 218 TRP 0.012 0.002 TRP C 74 HIS 0.004 0.001 HIS B 342 Details of bonding type rmsd covalent geometry : bond 0.00424 (12837) covalent geometry : angle 0.61046 (17433) SS BOND : bond 0.00704 ( 6) SS BOND : angle 1.79372 ( 12) hydrogen bonds : bond 0.04849 ( 552) hydrogen bonds : angle 5.67971 ( 1584) link_BETA1-4 : bond 0.00717 ( 6) link_BETA1-4 : angle 1.56066 ( 18) link_NAG-ASN : bond 0.00241 ( 1) link_NAG-ASN : angle 1.88273 ( 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: 28 poor density : 148 time to evaluate : 0.429 Fit side-chains REVERT: A 106 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7598 (pm20) REVERT: A 111 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7892 (mtmp) REVERT: A 199 ARG cc_start: 0.8398 (mtt-85) cc_final: 0.8172 (mtp180) REVERT: A 267 GLN cc_start: 0.7774 (tp40) cc_final: 0.7366 (mt0) REVERT: A 296 GLU cc_start: 0.8161 (tt0) cc_final: 0.7701 (tp30) REVERT: A 376 LYS cc_start: 0.7384 (mttp) cc_final: 0.6911 (tppt) REVERT: A 379 MET cc_start: 0.7442 (mtp) cc_final: 0.7020 (mtt) REVERT: B 95 GLN cc_start: 0.8526 (tt0) cc_final: 0.8184 (tt0) REVERT: B 106 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7623 (pm20) REVERT: B 111 LYS cc_start: 0.8374 (mtmm) cc_final: 0.8094 (mtmm) REVERT: B 132 ARG cc_start: 0.8368 (mmm160) cc_final: 0.8075 (mmt180) REVERT: B 199 ARG cc_start: 0.8179 (mtt-85) cc_final: 0.7962 (mtm110) REVERT: B 267 GLN cc_start: 0.7790 (tp40) cc_final: 0.7514 (mt0) REVERT: B 270 ILE cc_start: 0.8493 (mt) cc_final: 0.8269 (mm) REVERT: B 275 LYS cc_start: 0.7935 (mmtp) cc_final: 0.7655 (mtmt) REVERT: B 282 MET cc_start: 0.8930 (mtm) cc_final: 0.8695 (mtm) REVERT: B 296 GLU cc_start: 0.8137 (tt0) cc_final: 0.7852 (tp30) REVERT: B 338 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7234 (mt-10) REVERT: B 361 MET cc_start: 0.6280 (OUTLIER) cc_final: 0.4256 (mpt) REVERT: B 364 MET cc_start: 0.7553 (mtm) cc_final: 0.7253 (mtp) REVERT: B 421 ILE cc_start: 0.8594 (mm) cc_final: 0.8348 (mm) REVERT: B 487 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7275 (mm-30) REVERT: C 41 GLU cc_start: 0.8355 (tt0) cc_final: 0.7822 (mp0) REVERT: C 106 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7589 (pm20) REVERT: C 111 LYS cc_start: 0.8277 (mtmm) cc_final: 0.8008 (mtmm) REVERT: C 132 ARG cc_start: 0.8457 (mmm160) cc_final: 0.8161 (mmt180) REVERT: C 199 ARG cc_start: 0.8327 (mtt-85) cc_final: 0.8093 (mtm110) REVERT: C 296 GLU cc_start: 0.8174 (tt0) cc_final: 0.7598 (tp30) REVERT: C 459 MET cc_start: 0.7734 (mmm) cc_final: 0.7214 (mtm) outliers start: 28 outliers final: 15 residues processed: 165 average time/residue: 0.7228 time to fit residues: 128.2570 Evaluate side-chains 148 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 361 MET 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 130 optimal weight: 3.9990 chunk 139 optimal weight: 0.0040 chunk 143 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 8 optimal weight: 0.4980 chunk 63 optimal weight: 0.3980 chunk 128 optimal weight: 5.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3506 r_free = 0.3506 target = 0.139070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.115621 restraints weight = 12747.658| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.10 r_work: 0.3087 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12850 Z= 0.101 Angle : 0.519 5.412 17466 Z= 0.258 Chirality : 0.042 0.139 1957 Planarity : 0.004 0.044 2229 Dihedral : 6.736 51.996 1879 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.49 % Allowed : 12.98 % Favored : 85.53 % 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 aren not related in a simple way. whole: 0.72 (0.21), residues: 1590 helix: 1.76 (0.21), residues: 615 sheet: 0.26 (0.33), residues: 216 loop : -0.51 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 64 TYR 0.009 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 covalent geometry : bond 0.00233 (12837) covalent geometry : angle 0.51438 (17433) SS BOND : bond 0.00455 ( 6) SS BOND : angle 1.67371 ( 12) hydrogen bonds : bond 0.03604 ( 552) hydrogen bonds : angle 5.30740 ( 1584) link_BETA1-4 : bond 0.00673 ( 6) link_BETA1-4 : angle 1.69633 ( 18) link_NAG-ASN : bond 0.00114 ( 1) link_NAG-ASN : angle 1.31231 ( 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: 20 poor density : 143 time to evaluate : 0.532 Fit side-chains REVERT: A 106 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7484 (pm20) REVERT: A 111 LYS cc_start: 0.8150 (mtmm) cc_final: 0.7852 (mtmp) REVERT: A 199 ARG cc_start: 0.8387 (mtt-85) cc_final: 0.8153 (mtp180) REVERT: A 296 GLU cc_start: 0.8154 (tt0) cc_final: 0.7662 (tp30) REVERT: A 379 MET cc_start: 0.7423 (mtp) cc_final: 0.7132 (mtt) REVERT: B 95 GLN cc_start: 0.8510 (tt0) cc_final: 0.8143 (tt0) REVERT: B 106 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7602 (pm20) REVERT: B 111 LYS cc_start: 0.8250 (mtmm) cc_final: 0.7910 (mtmt) REVERT: B 132 ARG cc_start: 0.8270 (mmm160) cc_final: 0.7992 (mmt180) REVERT: B 270 ILE cc_start: 0.8440 (mt) cc_final: 0.8235 (mm) REVERT: B 275 LYS cc_start: 0.7916 (mmtp) cc_final: 0.7692 (mtmt) REVERT: B 282 MET cc_start: 0.8905 (mtm) cc_final: 0.8638 (mtm) REVERT: B 296 GLU cc_start: 0.8124 (tt0) cc_final: 0.7809 (tp30) REVERT: B 326 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.7825 (mmt) REVERT: B 364 MET cc_start: 0.7561 (mtm) cc_final: 0.7308 (mtp) REVERT: C 41 GLU cc_start: 0.8375 (tt0) cc_final: 0.7825 (mp0) REVERT: C 106 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7562 (pm20) REVERT: C 111 LYS cc_start: 0.8190 (mtmm) cc_final: 0.7871 (mtmm) REVERT: C 132 ARG cc_start: 0.8422 (mmm160) cc_final: 0.8192 (mmt180) REVERT: C 199 ARG cc_start: 0.8293 (mtt-85) cc_final: 0.8066 (mtm110) REVERT: C 296 GLU cc_start: 0.8113 (tt0) cc_final: 0.7542 (tp30) REVERT: C 379 MET cc_start: 0.7308 (mtm) cc_final: 0.7078 (mtt) REVERT: C 398 GLU cc_start: 0.6911 (tp30) cc_final: 0.6256 (tt0) REVERT: C 459 MET cc_start: 0.7668 (mmm) cc_final: 0.7179 (mtm) REVERT: C 471 GLU cc_start: 0.8434 (pm20) cc_final: 0.8180 (pm20) outliers start: 20 outliers final: 11 residues processed: 158 average time/residue: 0.7182 time to fit residues: 121.6962 Evaluate side-chains 141 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 B residue 457 SER 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: 2.9990 chunk 145 optimal weight: 4.9990 chunk 128 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 33 optimal weight: 0.0770 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3478 r_free = 0.3478 target = 0.136468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.113409 restraints weight = 12725.580| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.09 r_work: 0.3040 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12850 Z= 0.172 Angle : 0.597 7.386 17466 Z= 0.300 Chirality : 0.045 0.140 1957 Planarity : 0.004 0.044 2229 Dihedral : 5.976 52.733 1877 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.61 % Allowed : 12.30 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.20), residues: 1590 helix: 1.59 (0.21), residues: 612 sheet: 0.25 (0.33), residues: 216 loop : -0.60 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 171 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 covalent geometry : bond 0.00430 (12837) covalent geometry : angle 0.58967 (17433) SS BOND : bond 0.00250 ( 6) SS BOND : angle 2.97752 ( 12) hydrogen bonds : bond 0.04364 ( 552) hydrogen bonds : angle 5.39725 ( 1584) link_BETA1-4 : bond 0.00656 ( 6) link_BETA1-4 : angle 1.62554 ( 18) link_NAG-ASN : bond 0.00198 ( 1) link_NAG-ASN : angle 1.63856 ( 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 169 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.447 Fit side-chains REVERT: A 106 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7421 (pm20) REVERT: A 111 LYS cc_start: 0.8229 (mtmm) cc_final: 0.7902 (mtmp) REVERT: A 199 ARG cc_start: 0.8404 (mtt-85) cc_final: 0.8162 (mtp180) REVERT: A 296 GLU cc_start: 0.8151 (tt0) cc_final: 0.7655 (tp30) REVERT: A 376 LYS cc_start: 0.7467 (mttp) cc_final: 0.6980 (tppt) REVERT: A 379 MET cc_start: 0.7455 (mtp) cc_final: 0.7251 (mtt) REVERT: B 95 GLN cc_start: 0.8491 (tt0) cc_final: 0.8131 (tt0) REVERT: B 106 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7572 (pm20) REVERT: B 111 LYS cc_start: 0.8334 (mtmm) cc_final: 0.7933 (mtmt) REVERT: B 132 ARG cc_start: 0.8323 (mmm160) cc_final: 0.8015 (mmt180) REVERT: B 270 ILE cc_start: 0.8508 (mt) cc_final: 0.8269 (mm) REVERT: B 275 LYS cc_start: 0.8084 (mmtp) cc_final: 0.7766 (mtmt) REVERT: B 282 MET cc_start: 0.8913 (mtm) cc_final: 0.8633 (mtm) REVERT: B 296 GLU cc_start: 0.8153 (tt0) cc_final: 0.7794 (tp30) REVERT: B 326 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8179 (mmt) REVERT: B 363 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5750 (mp) REVERT: B 364 MET cc_start: 0.7625 (mtm) cc_final: 0.7380 (mtp) REVERT: B 487 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7327 (mm-30) REVERT: C 41 GLU cc_start: 0.8416 (tt0) cc_final: 0.7865 (mp0) REVERT: C 106 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7598 (pm20) REVERT: C 111 LYS cc_start: 0.8264 (mtmm) cc_final: 0.7983 (mtmm) REVERT: C 132 ARG cc_start: 0.8475 (mmm160) cc_final: 0.8241 (mmt180) REVERT: C 199 ARG cc_start: 0.8328 (mtt-85) cc_final: 0.8035 (mtm110) REVERT: C 296 GLU cc_start: 0.8123 (tt0) cc_final: 0.7546 (tp30) REVERT: C 379 MET cc_start: 0.7408 (mtm) cc_final: 0.7114 (mtt) REVERT: C 459 MET cc_start: 0.7794 (mmm) cc_final: 0.7278 (mtm) outliers start: 35 outliers final: 16 residues processed: 161 average time/residue: 0.7347 time to fit residues: 127.1428 Evaluate side-chains 145 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 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 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 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: 0.9990 chunk 74 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 135 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3488 r_free = 0.3488 target = 0.137420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.113832 restraints weight = 12834.720| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.12 r_work: 0.3062 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12850 Z= 0.123 Angle : 0.541 5.883 17466 Z= 0.273 Chirality : 0.042 0.146 1957 Planarity : 0.004 0.045 2229 Dihedral : 5.591 52.949 1877 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.46 % Allowed : 13.05 % Favored : 84.49 % 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 aren not related in a simple way. whole: 0.63 (0.20), residues: 1590 helix: 1.72 (0.21), residues: 612 sheet: 0.24 (0.33), residues: 216 loop : -0.59 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.011 0.001 TYR B 152 PHE 0.016 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 covalent geometry : bond 0.00298 (12837) covalent geometry : angle 0.53471 (17433) SS BOND : bond 0.00199 ( 6) SS BOND : angle 2.81267 ( 12) hydrogen bonds : bond 0.03740 ( 552) hydrogen bonds : angle 5.25472 ( 1584) link_BETA1-4 : bond 0.00609 ( 6) link_BETA1-4 : angle 1.38465 ( 18) link_NAG-ASN : bond 0.00118 ( 1) link_NAG-ASN : angle 1.52100 ( 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 165 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.544 Fit side-chains REVERT: A 106 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7397 (pm20) REVERT: A 111 LYS cc_start: 0.8190 (mtmm) cc_final: 0.7866 (mtmp) REVERT: A 199 ARG cc_start: 0.8416 (mtt-85) cc_final: 0.8163 (mtp180) REVERT: A 296 GLU cc_start: 0.8178 (tt0) cc_final: 0.7664 (tp30) REVERT: A 326 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8011 (mmt) REVERT: A 376 LYS cc_start: 0.7461 (mttp) cc_final: 0.6955 (tppt) REVERT: A 379 MET cc_start: 0.7437 (mtp) cc_final: 0.7231 (mtt) REVERT: B 92 LYS cc_start: 0.8419 (mttp) cc_final: 0.7852 (mtmm) REVERT: B 95 GLN cc_start: 0.8493 (tt0) cc_final: 0.8037 (tt0) REVERT: B 106 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7558 (pm20) REVERT: B 111 LYS cc_start: 0.8331 (mtmm) cc_final: 0.7919 (mtmt) REVERT: B 132 ARG cc_start: 0.8293 (mmm160) cc_final: 0.7994 (mmt180) REVERT: B 270 ILE cc_start: 0.8462 (mt) cc_final: 0.8236 (mm) REVERT: B 275 LYS cc_start: 0.7513 (mmtp) cc_final: 0.7195 (mtmt) REVERT: B 282 MET cc_start: 0.8875 (mtm) cc_final: 0.8627 (mtm) REVERT: B 296 GLU cc_start: 0.8160 (tt0) cc_final: 0.7914 (tp30) REVERT: B 363 LEU cc_start: 0.5955 (OUTLIER) cc_final: 0.5523 (mp) REVERT: B 364 MET cc_start: 0.7608 (mtm) cc_final: 0.7336 (mtp) REVERT: B 487 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7298 (mm-30) REVERT: C 41 GLU cc_start: 0.8488 (tt0) cc_final: 0.7944 (mp0) REVERT: C 106 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7527 (pm20) REVERT: C 111 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7962 (mtmm) REVERT: C 132 ARG cc_start: 0.8471 (mmm160) cc_final: 0.8239 (mmt180) REVERT: C 199 ARG cc_start: 0.8324 (mtt-85) cc_final: 0.8100 (mtm110) REVERT: C 296 GLU cc_start: 0.8164 (tt0) cc_final: 0.7552 (tp30) REVERT: C 379 MET cc_start: 0.7335 (mtm) cc_final: 0.7124 (mtt) REVERT: C 398 GLU cc_start: 0.6945 (tp30) cc_final: 0.6297 (tt0) REVERT: C 459 MET cc_start: 0.7769 (mmm) cc_final: 0.7262 (mtm) outliers start: 33 outliers final: 17 residues processed: 159 average time/residue: 0.7171 time to fit residues: 123.2375 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 : 0.515 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 115 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 64 optimal weight: 0.0870 chunk 52 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3500 r_free = 0.3500 target = 0.138446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.114951 restraints weight = 12723.205| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.12 r_work: 0.3079 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12850 Z= 0.114 Angle : 0.529 5.613 17466 Z= 0.266 Chirality : 0.042 0.127 1957 Planarity : 0.004 0.046 2229 Dihedral : 5.494 53.123 1877 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.39 % Allowed : 13.72 % Favored : 83.89 % 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 aren not related in a simple way. whole: 0.69 (0.21), residues: 1590 helix: 1.79 (0.21), residues: 612 sheet: 0.24 (0.33), residues: 216 loop : -0.57 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 287 TYR 0.010 0.001 TYR B 152 PHE 0.019 0.001 PHE A 218 TRP 0.010 0.001 TRP B 357 HIS 0.003 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00274 (12837) covalent geometry : angle 0.52505 (17433) SS BOND : bond 0.00194 ( 6) SS BOND : angle 2.01961 ( 12) hydrogen bonds : bond 0.03570 ( 552) hydrogen bonds : angle 5.20168 ( 1584) link_BETA1-4 : bond 0.00596 ( 6) link_BETA1-4 : angle 1.30293 ( 18) link_NAG-ASN : bond 0.00124 ( 1) link_NAG-ASN : angle 1.51143 ( 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 167 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.544 Fit side-chains REVERT: A 106 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7372 (pm20) REVERT: A 111 LYS cc_start: 0.8176 (mtmm) cc_final: 0.7863 (mtmp) REVERT: A 296 GLU cc_start: 0.8134 (tt0) cc_final: 0.7627 (tp30) REVERT: A 326 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.7882 (mmt) REVERT: A 376 LYS cc_start: 0.7421 (mttp) cc_final: 0.6907 (tppt) REVERT: A 379 MET cc_start: 0.7433 (mtp) cc_final: 0.7151 (mtt) REVERT: B 95 GLN cc_start: 0.8492 (tt0) cc_final: 0.8153 (tt0) REVERT: B 106 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7551 (pm20) REVERT: B 111 LYS cc_start: 0.8293 (mtmm) cc_final: 0.7906 (mtmt) REVERT: B 132 ARG cc_start: 0.8303 (mmm160) cc_final: 0.8024 (mmt180) REVERT: B 270 ILE cc_start: 0.8490 (mt) cc_final: 0.8271 (mm) REVERT: B 275 LYS cc_start: 0.7419 (mmtp) cc_final: 0.7124 (mtmt) REVERT: B 282 MET cc_start: 0.8888 (mtm) cc_final: 0.8646 (mtm) REVERT: B 296 GLU cc_start: 0.8144 (tt0) cc_final: 0.7898 (tp30) REVERT: B 326 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.7584 (mmp) REVERT: B 363 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.5462 (mp) REVERT: B 364 MET cc_start: 0.7591 (mtm) cc_final: 0.7337 (mtp) REVERT: B 487 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7170 (mm-30) REVERT: C 41 GLU cc_start: 0.8474 (tt0) cc_final: 0.7928 (mp0) REVERT: C 106 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7545 (pm20) REVERT: C 111 LYS cc_start: 0.8229 (mtmm) cc_final: 0.7951 (mtmm) REVERT: C 132 ARG cc_start: 0.8484 (mmm160) cc_final: 0.8267 (mmt180) REVERT: C 199 ARG cc_start: 0.8322 (mtt-85) cc_final: 0.8091 (mtm110) REVERT: C 296 GLU cc_start: 0.8141 (tt0) cc_final: 0.7532 (tp30) REVERT: C 379 MET cc_start: 0.7345 (mtm) cc_final: 0.7141 (mtt) REVERT: C 398 GLU cc_start: 0.6941 (tp30) cc_final: 0.6323 (tt0) REVERT: C 459 MET cc_start: 0.7758 (mmm) cc_final: 0.7252 (mtm) REVERT: C 487 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7860 (tp30) outliers start: 32 outliers final: 20 residues processed: 160 average time/residue: 0.7256 time to fit residues: 125.1291 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 : 0.350 ------------------------------------------------------------------------------- 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 A residue 483 GLU 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 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 444 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 32 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 56 optimal weight: 0.0570 chunk 61 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 25 optimal weight: 0.0270 chunk 149 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3531 r_free = 0.3531 target = 0.141158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.117884 restraints weight = 12563.583| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.11 r_work: 0.3104 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12850 Z= 0.090 Angle : 0.497 5.038 17466 Z= 0.249 Chirality : 0.041 0.130 1957 Planarity : 0.004 0.046 2229 Dihedral : 5.294 53.043 1877 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.16 % Allowed : 14.02 % Favored : 83.82 % 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 aren not related in a simple way. whole: 0.87 (0.21), residues: 1590 helix: 1.94 (0.22), residues: 615 sheet: 0.12 (0.31), residues: 246 loop : -0.40 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 199 TYR 0.007 0.001 TYR A 447 PHE 0.016 0.001 PHE A 218 TRP 0.010 0.001 TRP B 547 HIS 0.002 0.000 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00207 (12837) covalent geometry : angle 0.49227 (17433) SS BOND : bond 0.00247 ( 6) SS BOND : angle 2.10465 ( 12) hydrogen bonds : bond 0.03108 ( 552) hydrogen bonds : angle 5.06675 ( 1584) link_BETA1-4 : bond 0.00567 ( 6) link_BETA1-4 : angle 1.25040 ( 18) link_NAG-ASN : bond 0.00095 ( 1) link_NAG-ASN : angle 1.39141 ( 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 167 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.560 Fit side-chains REVERT: A 106 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7357 (pm20) REVERT: A 111 LYS cc_start: 0.8123 (mtmm) cc_final: 0.7835 (mtmp) REVERT: A 296 GLU cc_start: 0.8116 (tt0) cc_final: 0.7602 (tp30) REVERT: A 326 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.7576 (mmt) REVERT: A 366 TYR cc_start: 0.6732 (OUTLIER) cc_final: 0.5003 (t80) REVERT: A 379 MET cc_start: 0.7353 (mtp) cc_final: 0.7118 (mtt) REVERT: A 487 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7554 (tp30) REVERT: B 69 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8020 (mt0) REVERT: B 95 GLN cc_start: 0.8491 (tt0) cc_final: 0.8161 (tt0) REVERT: B 106 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7578 (pm20) REVERT: B 111 LYS cc_start: 0.8255 (mtmm) cc_final: 0.7884 (mtmt) REVERT: B 132 ARG cc_start: 0.8296 (mmm160) cc_final: 0.8038 (mmt180) REVERT: B 275 LYS cc_start: 0.7180 (mmtp) cc_final: 0.6913 (mtmt) REVERT: B 282 MET cc_start: 0.8890 (mtm) cc_final: 0.8637 (mtm) REVERT: B 296 GLU cc_start: 0.8137 (tt0) cc_final: 0.7883 (tp30) REVERT: B 326 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8481 (mmm) REVERT: B 363 LEU cc_start: 0.5680 (OUTLIER) cc_final: 0.5272 (mp) REVERT: B 364 MET cc_start: 0.7560 (mtm) cc_final: 0.7320 (mtp) REVERT: C 41 GLU cc_start: 0.8457 (tt0) cc_final: 0.8001 (mp0) REVERT: C 106 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7534 (pm20) REVERT: C 111 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7856 (mtmm) REVERT: C 199 ARG cc_start: 0.8325 (mtt-85) cc_final: 0.8108 (mtm110) REVERT: C 296 GLU cc_start: 0.8141 (tt0) cc_final: 0.7528 (tp30) REVERT: C 398 GLU cc_start: 0.6917 (tp30) cc_final: 0.6362 (tt0) REVERT: C 459 MET cc_start: 0.7684 (mmm) cc_final: 0.7283 (mtm) REVERT: C 487 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7814 (tp30) outliers start: 29 outliers final: 10 residues processed: 161 average time/residue: 0.7360 time to fit residues: 127.6839 Evaluate side-chains 143 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 366 TYR 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 218 PHE 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 C residue 34 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 301 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 120 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 111 optimal weight: 0.1980 chunk 154 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3507 r_free = 0.3507 target = 0.139046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.115701 restraints weight = 12624.855| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.10 r_work: 0.3094 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12850 Z= 0.115 Angle : 0.531 6.345 17466 Z= 0.266 Chirality : 0.042 0.129 1957 Planarity : 0.004 0.046 2229 Dihedral : 5.332 53.239 1875 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.16 % Allowed : 14.17 % 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 aren not related in a simple way. whole: 0.83 (0.21), residues: 1590 helix: 1.88 (0.21), residues: 615 sheet: 0.12 (0.31), residues: 246 loop : -0.40 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 199 TYR 0.011 0.001 TYR B 152 PHE 0.019 0.001 PHE C 218 TRP 0.014 0.001 TRP B 357 HIS 0.003 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00277 (12837) covalent geometry : angle 0.52354 (17433) SS BOND : bond 0.00245 ( 6) SS BOND : angle 2.93446 ( 12) hydrogen bonds : bond 0.03501 ( 552) hydrogen bonds : angle 5.13188 ( 1584) link_BETA1-4 : bond 0.00610 ( 6) link_BETA1-4 : angle 1.29997 ( 18) link_NAG-ASN : bond 0.00095 ( 1) link_NAG-ASN : angle 1.45865 ( 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 158 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.509 Fit side-chains REVERT: A 106 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7360 (pm20) REVERT: A 111 LYS cc_start: 0.8140 (mtmm) cc_final: 0.7883 (mtmp) REVERT: A 296 GLU cc_start: 0.8156 (tt0) cc_final: 0.7637 (tp30) REVERT: A 326 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.7936 (mmt) REVERT: A 366 TYR cc_start: 0.6681 (OUTLIER) cc_final: 0.4913 (t80) REVERT: A 379 MET cc_start: 0.7393 (mtp) cc_final: 0.7148 (mtt) REVERT: A 487 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7652 (tp30) REVERT: B 69 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8030 (mt0) REVERT: B 95 GLN cc_start: 0.8465 (tt0) cc_final: 0.8128 (tt0) REVERT: B 106 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7612 (pm20) REVERT: B 111 LYS cc_start: 0.8267 (mtmm) cc_final: 0.7911 (mtmt) REVERT: B 132 ARG cc_start: 0.8308 (mmm160) cc_final: 0.8054 (mmt180) REVERT: B 275 LYS cc_start: 0.7137 (mmtp) cc_final: 0.6892 (mtmt) REVERT: B 282 MET cc_start: 0.8892 (mtm) cc_final: 0.8635 (mtm) REVERT: B 296 GLU cc_start: 0.8143 (tt0) cc_final: 0.7772 (tp30) REVERT: B 326 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.7576 (mmp) REVERT: B 363 LEU cc_start: 0.5621 (OUTLIER) cc_final: 0.5237 (mp) REVERT: C 41 GLU cc_start: 0.8425 (tt0) cc_final: 0.7970 (mp0) REVERT: C 106 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7524 (pm20) REVERT: C 111 LYS cc_start: 0.8197 (mtmm) cc_final: 0.7868 (mtmm) REVERT: C 199 ARG cc_start: 0.8352 (mtt-85) cc_final: 0.8116 (mtm110) REVERT: C 296 GLU cc_start: 0.8155 (tt0) cc_final: 0.7537 (tp30) REVERT: C 398 GLU cc_start: 0.6970 (tp30) cc_final: 0.6337 (tt0) REVERT: C 459 MET cc_start: 0.7724 (mmm) cc_final: 0.7343 (mtm) REVERT: C 487 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7792 (tp30) outliers start: 29 outliers final: 17 residues processed: 152 average time/residue: 0.7105 time to fit residues: 116.4967 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 : 0.439 ------------------------------------------------------------------------------- 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 366 TYR 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 32 LYS 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 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 C residue 34 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 363 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 0.0170 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 86 optimal weight: 0.0470 chunk 13 optimal weight: 4.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3516 r_free = 0.3516 target = 0.139878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.114983 restraints weight = 12596.179| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.27 r_work: 0.3085 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12850 Z= 0.113 Angle : 0.538 9.138 17466 Z= 0.270 Chirality : 0.042 0.128 1957 Planarity : 0.004 0.046 2229 Dihedral : 5.438 53.373 1875 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.94 % Allowed : 14.54 % Favored : 83.52 % 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 aren not related in a simple way. whole: 0.82 (0.21), residues: 1590 helix: 1.89 (0.21), residues: 612 sheet: 0.13 (0.31), residues: 246 loop : -0.43 (0.22), residues: 732 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 0.020 0.001 PHE C 218 TRP 0.010 0.001 TRP B 357 HIS 0.003 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00273 (12837) covalent geometry : angle 0.52985 (17433) SS BOND : bond 0.00298 ( 6) SS BOND : angle 3.27191 ( 12) hydrogen bonds : bond 0.03465 ( 552) hydrogen bonds : angle 5.10834 ( 1584) link_BETA1-4 : bond 0.00596 ( 6) link_BETA1-4 : angle 1.26951 ( 18) link_NAG-ASN : bond 0.00106 ( 1) link_NAG-ASN : angle 1.50374 ( 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 155 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7335 (pm20) REVERT: A 111 LYS cc_start: 0.8160 (mtmm) cc_final: 0.7889 (mtmp) REVERT: A 296 GLU cc_start: 0.8131 (tt0) cc_final: 0.7625 (tp30) REVERT: A 326 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.7886 (mmt) REVERT: A 352 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.7481 (ttmt) REVERT: A 379 MET cc_start: 0.7411 (mtp) cc_final: 0.7162 (mtt) REVERT: A 487 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7645 (tp30) REVERT: B 69 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8038 (mt0) REVERT: B 95 GLN cc_start: 0.8466 (tt0) cc_final: 0.8128 (tt0) REVERT: B 106 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7591 (pm20) REVERT: B 111 LYS cc_start: 0.8267 (mtmm) cc_final: 0.7901 (mtmt) REVERT: B 132 ARG cc_start: 0.8336 (mmm160) cc_final: 0.8090 (mmt180) REVERT: B 275 LYS cc_start: 0.7182 (mmtp) cc_final: 0.6902 (mtmt) REVERT: B 282 MET cc_start: 0.8902 (mtm) cc_final: 0.8639 (mtm) REVERT: B 296 GLU cc_start: 0.8127 (tt0) cc_final: 0.7899 (tp30) REVERT: B 326 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.7508 (mmp) REVERT: B 363 LEU cc_start: 0.5696 (OUTLIER) cc_final: 0.5351 (mp) REVERT: C 41 GLU cc_start: 0.8470 (tt0) cc_final: 0.7956 (mp0) REVERT: C 106 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7527 (pm20) REVERT: C 111 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7889 (mtmm) REVERT: C 199 ARG cc_start: 0.8325 (mtt-85) cc_final: 0.8125 (mtm110) REVERT: C 285 CYS cc_start: 0.7193 (m) cc_final: 0.6897 (t) REVERT: C 296 GLU cc_start: 0.8150 (tt0) cc_final: 0.7527 (tp30) REVERT: C 398 GLU cc_start: 0.6972 (tp30) cc_final: 0.6347 (tt0) REVERT: C 459 MET cc_start: 0.7656 (mmm) cc_final: 0.7252 (mtm) REVERT: C 487 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7762 (tp30) outliers start: 26 outliers final: 16 residues processed: 149 average time/residue: 0.7655 time to fit residues: 122.6558 Evaluate side-chains 150 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 352 LYS 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 32 LYS 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 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 C residue 34 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 301 MET 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: 3.9990 chunk 5 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 GLN B 267 GLN B 340 ASN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.135767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.112114 restraints weight = 12753.612| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.13 r_work: 0.3035 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 12850 Z= 0.218 Angle : 0.657 10.234 17466 Z= 0.332 Chirality : 0.047 0.144 1957 Planarity : 0.005 0.047 2229 Dihedral : 5.861 54.515 1875 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.79 % Allowed : 14.91 % Favored : 83.30 % 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 aren not related in a simple way. whole: 0.41 (0.20), residues: 1590 helix: 1.46 (0.21), residues: 612 sheet: 0.27 (0.32), residues: 216 loop : -0.69 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 171 TYR 0.018 0.002 TYR C 152 PHE 0.020 0.002 PHE C 218 TRP 0.010 0.002 TRP B 74 HIS 0.006 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00553 (12837) covalent geometry : angle 0.64663 (17433) SS BOND : bond 0.00377 ( 6) SS BOND : angle 4.09291 ( 12) hydrogen bonds : bond 0.04691 ( 552) hydrogen bonds : angle 5.36738 ( 1584) link_BETA1-4 : bond 0.00703 ( 6) link_BETA1-4 : angle 1.34381 ( 18) link_NAG-ASN : bond 0.00196 ( 1) link_NAG-ASN : angle 2.00827 ( 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 154 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.469 Fit side-chains REVERT: A 106 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7432 (pm20) REVERT: A 111 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7877 (mtmp) REVERT: A 326 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8246 (mmt) REVERT: A 352 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.7519 (ttmt) REVERT: A 376 LYS cc_start: 0.7557 (mttp) cc_final: 0.7033 (tppt) REVERT: A 379 MET cc_start: 0.7471 (mtp) cc_final: 0.7200 (mtt) REVERT: B 69 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8062 (mt0) REVERT: B 95 GLN cc_start: 0.8514 (tt0) cc_final: 0.8177 (tt0) REVERT: B 106 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7581 (pm20) REVERT: B 111 LYS cc_start: 0.8272 (mtmm) cc_final: 0.7930 (mtmm) REVERT: B 132 ARG cc_start: 0.8370 (mmm160) cc_final: 0.8109 (mmt180) REVERT: B 275 LYS cc_start: 0.7475 (mmtp) cc_final: 0.7193 (mtmt) REVERT: B 296 GLU cc_start: 0.8223 (tt0) cc_final: 0.7838 (tp30) REVERT: B 326 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8085 (mmt) REVERT: B 363 LEU cc_start: 0.5509 (OUTLIER) cc_final: 0.5202 (mp) REVERT: B 421 ILE cc_start: 0.8558 (mm) cc_final: 0.8284 (mm) REVERT: C 41 GLU cc_start: 0.8445 (tt0) cc_final: 0.7974 (mp0) REVERT: C 106 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7514 (pm20) REVERT: C 111 LYS cc_start: 0.8300 (mtmm) cc_final: 0.8021 (mtmm) REVERT: C 199 ARG cc_start: 0.8342 (mtt-85) cc_final: 0.8113 (mtm110) REVERT: C 296 GLU cc_start: 0.8197 (tt0) cc_final: 0.7598 (tp30) REVERT: C 398 GLU cc_start: 0.7049 (tp30) cc_final: 0.6322 (tt0) REVERT: C 459 MET cc_start: 0.7772 (mmm) cc_final: 0.7339 (mtm) outliers start: 24 outliers final: 16 residues processed: 149 average time/residue: 0.7818 time to fit residues: 124.9449 Evaluate side-chains 149 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 352 LYS Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 32 LYS 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 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 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 301 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 85 optimal weight: 0.8980 chunk 127 optimal weight: 0.3980 chunk 154 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 133 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 340 ASN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 267 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.136112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.110271 restraints weight = 12738.341| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.39 r_work: 0.3047 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 12850 Z= 0.198 Angle : 0.894 59.200 17466 Z= 0.503 Chirality : 0.044 0.139 1957 Planarity : 0.005 0.046 2229 Dihedral : 5.871 54.554 1875 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.72 % Allowed : 15.36 % Favored : 82.92 % 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 aren not related in a simple way. whole: 0.38 (0.20), residues: 1590 helix: 1.45 (0.21), residues: 612 sheet: 0.27 (0.32), 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 0.016 0.002 TYR C 152 PHE 0.020 0.002 PHE C 218 TRP 0.011 0.002 TRP B 74 HIS 0.005 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00453 (12837) covalent geometry : angle 0.88771 (17433) SS BOND : bond 0.00099 ( 6) SS BOND : angle 3.87460 ( 12) hydrogen bonds : bond 0.04497 ( 552) hydrogen bonds : angle 5.35938 ( 1584) link_BETA1-4 : bond 0.00654 ( 6) link_BETA1-4 : angle 1.33719 ( 18) link_NAG-ASN : bond 0.00262 ( 1) link_NAG-ASN : angle 2.02101 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4322.88 seconds wall clock time: 74 minutes 35.18 seconds (4475.18 seconds total)