Starting phenix.real_space_refine on Wed Jul 30 19:09:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eor_28465/07_2025/8eor_28465.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eor_28465/07_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_28465/07_2025/8eor_28465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eor_28465/07_2025/8eor_28465.map" model { file = "/net/cci-nas-00/data/ceres_data/8eor_28465/07_2025/8eor_28465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eor_28465/07_2025/8eor_28465.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.061 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.76, per 1000 atoms: 0.62 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: 3.26 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.38 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: 3.81 Time building geometry restraints manager: 3.71 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.500 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 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 TRP 0.007 0.001 TRP B 74 HIS 0.002 0.001 HIS C 140 PHE 0.010 0.001 PHE A 177 TYR 0.010 0.001 TYR C 152 ARG 0.003 0.000 ARG C 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 1) link_NAG-ASN : angle 1.22956 ( 3) link_BETA1-4 : bond 0.00424 ( 6) link_BETA1-4 : angle 1.31775 ( 18) hydrogen bonds : bond 0.16382 ( 552) hydrogen bonds : angle 7.18455 ( 1584) SS BOND : bond 0.00230 ( 6) SS BOND : angle 0.77016 ( 12) covalent geometry : bond 0.00390 (12837) covalent geometry : angle 0.63803 (17433) *********************** 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 : 1.371 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: 1.5075 time to fit residues: 371.1415 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 : 1.484 ------------------------------------------------------------------------------- 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 134 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 144 optimal weight: 0.0060 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN B 340 ASN C 169 GLN C 372 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.138235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.115446 restraints weight = 12610.216| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.02 r_work: 0.3078 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12850 Z= 0.130 Angle : 0.562 7.265 17466 Z= 0.282 Chirality : 0.043 0.131 1957 Planarity : 0.004 0.040 2229 Dihedral : 9.143 70.239 1879 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.72 % Allowed : 11.11 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.21), residues: 1590 helix: 1.60 (0.21), residues: 615 sheet: 0.40 (0.34), residues: 216 loop : -0.52 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 547 HIS 0.004 0.001 HIS B 342 PHE 0.018 0.001 PHE A 218 TYR 0.012 0.001 TYR A 152 ARG 0.002 0.000 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 1) link_NAG-ASN : angle 1.54899 ( 3) link_BETA1-4 : bond 0.00669 ( 6) link_BETA1-4 : angle 1.57355 ( 18) hydrogen bonds : bond 0.04417 ( 552) hydrogen bonds : angle 5.60128 ( 1584) SS BOND : bond 0.00332 ( 6) SS BOND : angle 1.90010 ( 12) covalent geometry : bond 0.00293 (12837) covalent geometry : angle 0.55774 (17433) *********************** 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 171 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 1.601 Fit side-chains REVERT: A 57 LYS cc_start: 0.8697 (tttt) cc_final: 0.8431 (tttt) REVERT: A 86 MET cc_start: 0.8820 (ptt) cc_final: 0.8597 (ptt) REVERT: A 106 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7570 (pm20) REVERT: A 111 LYS cc_start: 0.8058 (mtmm) cc_final: 0.7856 (mtmp) REVERT: A 199 ARG cc_start: 0.8383 (mtt-85) cc_final: 0.8158 (mtp180) REVERT: A 267 GLN cc_start: 0.7711 (tp40) cc_final: 0.7325 (mt0) REVERT: A 296 GLU cc_start: 0.8105 (tt0) cc_final: 0.7674 (tp30) REVERT: A 379 MET cc_start: 0.7478 (mtp) cc_final: 0.7135 (mtt) REVERT: A 487 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7739 (tp30) REVERT: B 95 GLN cc_start: 0.8492 (tt0) cc_final: 0.8131 (tt0) REVERT: B 106 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7610 (pm20) REVERT: B 111 LYS cc_start: 0.8304 (mtmm) cc_final: 0.8004 (mtmt) REVERT: B 132 ARG cc_start: 0.8318 (mmm160) cc_final: 0.8073 (mmt180) REVERT: B 267 GLN cc_start: 0.7682 (tp40) cc_final: 0.7415 (mt0) REVERT: B 275 LYS cc_start: 0.7917 (mmtp) cc_final: 0.7647 (mtmt) REVERT: B 282 MET cc_start: 0.8923 (mtm) cc_final: 0.8628 (mtm) REVERT: B 296 GLU cc_start: 0.8070 (tt0) cc_final: 0.7837 (tp30) REVERT: B 361 MET cc_start: 0.6357 (OUTLIER) cc_final: 0.4295 (mpt) REVERT: B 364 MET cc_start: 0.7549 (mtm) cc_final: 0.7256 (mtp) REVERT: C 41 GLU cc_start: 0.8341 (tt0) cc_final: 0.7831 (mp0) REVERT: C 106 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7577 (pm20) REVERT: C 111 LYS cc_start: 0.8222 (mtmm) cc_final: 0.7980 (mtmm) REVERT: C 132 ARG cc_start: 0.8420 (mmm160) cc_final: 0.8207 (mmt180) REVERT: C 199 ARG cc_start: 0.8282 (mtt-85) cc_final: 0.8074 (mtm110) REVERT: C 296 GLU cc_start: 0.8072 (tt0) cc_final: 0.7584 (tp30) REVERT: C 459 MET cc_start: 0.7728 (mmm) cc_final: 0.7281 (mtm) outliers start: 23 outliers final: 12 residues processed: 163 average time/residue: 1.8324 time to fit residues: 321.1545 Evaluate side-chains 145 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 68 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 151 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 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 = 0.3480 r_free = 0.3480 target = 0.136842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.113720 restraints weight = 12828.635| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.10 r_work: 0.3055 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12850 Z= 0.157 Angle : 0.586 7.240 17466 Z= 0.294 Chirality : 0.045 0.139 1957 Planarity : 0.004 0.043 2229 Dihedral : 6.901 52.626 1878 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.31 % Allowed : 12.08 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.20), residues: 1590 helix: 1.56 (0.21), residues: 612 sheet: 0.22 (0.33), residues: 216 loop : -0.58 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 74 HIS 0.003 0.001 HIS C 140 PHE 0.019 0.002 PHE A 218 TYR 0.015 0.002 TYR B 152 ARG 0.005 0.000 ARG C 171 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 1) link_NAG-ASN : angle 1.66953 ( 3) link_BETA1-4 : bond 0.00736 ( 6) link_BETA1-4 : angle 1.70285 ( 18) hydrogen bonds : bond 0.04425 ( 552) hydrogen bonds : angle 5.44419 ( 1584) SS BOND : bond 0.00260 ( 6) SS BOND : angle 1.68241 ( 12) covalent geometry : bond 0.00387 (12837) covalent geometry : angle 0.58226 (17433) *********************** 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 165 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 1.344 Fit side-chains REVERT: A 106 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7473 (pm20) REVERT: A 111 LYS cc_start: 0.8213 (mtmm) cc_final: 0.7880 (mtmp) REVERT: A 199 ARG cc_start: 0.8399 (mtt-85) cc_final: 0.8149 (mtp180) REVERT: A 296 GLU cc_start: 0.8187 (tt0) cc_final: 0.7691 (tp30) REVERT: A 376 LYS cc_start: 0.7474 (mttp) cc_final: 0.6942 (tppt) REVERT: A 379 MET cc_start: 0.7501 (mtp) cc_final: 0.7176 (mtt) REVERT: A 446 MET cc_start: 0.9080 (mtp) cc_final: 0.8855 (mtp) REVERT: B 95 GLN cc_start: 0.8503 (tt0) cc_final: 0.8129 (tt0) REVERT: B 106 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7601 (pm20) REVERT: B 111 LYS cc_start: 0.8386 (mtmm) cc_final: 0.8024 (mtmt) REVERT: B 132 ARG cc_start: 0.8303 (mmm160) cc_final: 0.7983 (mmt180) REVERT: B 267 GLN cc_start: 0.7892 (tp40) cc_final: 0.7555 (mt0) REVERT: B 275 LYS cc_start: 0.7997 (mmtp) cc_final: 0.7762 (mtmt) REVERT: B 282 MET cc_start: 0.8934 (mtm) cc_final: 0.8712 (mtm) REVERT: B 296 GLU cc_start: 0.8151 (tt0) cc_final: 0.7806 (tp30) REVERT: B 326 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8124 (mmt) REVERT: B 364 MET cc_start: 0.7598 (mtm) cc_final: 0.7313 (mtp) REVERT: B 487 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7302 (mm-30) REVERT: C 41 GLU cc_start: 0.8404 (tt0) cc_final: 0.7857 (mp0) REVERT: C 106 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7569 (pm20) REVERT: C 111 LYS cc_start: 0.8311 (mtmm) cc_final: 0.8046 (mtmm) REVERT: C 132 ARG cc_start: 0.8484 (mmm160) cc_final: 0.8130 (mmt180) REVERT: C 199 ARG cc_start: 0.8324 (mtt-85) cc_final: 0.8033 (mtm110) REVERT: C 296 GLU cc_start: 0.8130 (tt0) cc_final: 0.7560 (tp30) REVERT: C 379 MET cc_start: 0.7360 (mtm) cc_final: 0.7119 (mtt) REVERT: C 459 MET cc_start: 0.7686 (mmm) cc_final: 0.7184 (mtm) outliers start: 31 outliers final: 19 residues processed: 156 average time/residue: 1.4178 time to fit residues: 238.8136 Evaluate side-chains 146 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 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 380 SER Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 532 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 107 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 106 optimal weight: 0.5980 chunk 88 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.136976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.113638 restraints weight = 12463.042| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.09 r_work: 0.3060 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12850 Z= 0.170 Angle : 0.595 7.242 17466 Z= 0.299 Chirality : 0.045 0.136 1957 Planarity : 0.005 0.044 2229 Dihedral : 5.928 53.122 1878 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.61 % Allowed : 12.98 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.20), residues: 1590 helix: 1.48 (0.21), residues: 612 sheet: 0.22 (0.33), residues: 216 loop : -0.65 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 74 HIS 0.003 0.001 HIS C 140 PHE 0.017 0.002 PHE A 218 TYR 0.015 0.002 TYR B 152 ARG 0.003 0.000 ARG C 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 1) link_NAG-ASN : angle 1.83640 ( 3) link_BETA1-4 : bond 0.00659 ( 6) link_BETA1-4 : angle 1.49197 ( 18) hydrogen bonds : bond 0.04396 ( 552) hydrogen bonds : angle 5.40584 ( 1584) SS BOND : bond 0.00272 ( 6) SS BOND : angle 2.42774 ( 12) covalent geometry : bond 0.00424 (12837) covalent geometry : angle 0.58933 (17433) *********************** 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 : 2.009 Fit side-chains REVERT: A 106 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7480 (pm20) REVERT: A 111 LYS cc_start: 0.8217 (mtmm) cc_final: 0.7919 (mtmp) REVERT: A 199 ARG cc_start: 0.8393 (mtt-85) cc_final: 0.8162 (mtp180) REVERT: A 376 LYS cc_start: 0.7456 (mttp) cc_final: 0.7004 (tppt) REVERT: A 379 MET cc_start: 0.7432 (mtp) cc_final: 0.7209 (mtt) REVERT: B 95 GLN cc_start: 0.8517 (tt0) cc_final: 0.8146 (tt0) REVERT: B 106 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7592 (pm20) REVERT: B 111 LYS cc_start: 0.8336 (mtmm) cc_final: 0.7937 (mtmt) REVERT: B 132 ARG cc_start: 0.8319 (mmm160) cc_final: 0.7993 (mmt180) REVERT: B 267 GLN cc_start: 0.7899 (tp40) cc_final: 0.7558 (mt0) REVERT: B 275 LYS cc_start: 0.8028 (mmtp) cc_final: 0.7712 (mtmt) REVERT: B 282 MET cc_start: 0.8939 (mtm) cc_final: 0.8718 (mtm) REVERT: B 296 GLU cc_start: 0.8167 (tt0) cc_final: 0.7801 (tp30) REVERT: B 326 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8493 (mmt) REVERT: B 363 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.5676 (mp) REVERT: B 364 MET cc_start: 0.7633 (mtm) cc_final: 0.7347 (mtp) REVERT: B 487 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7289 (mm-30) REVERT: C 41 GLU cc_start: 0.8381 (tt0) cc_final: 0.7858 (mp0) REVERT: C 106 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7602 (pm20) REVERT: C 111 LYS cc_start: 0.8270 (mtmm) cc_final: 0.7982 (mtmm) REVERT: C 132 ARG cc_start: 0.8496 (mmm160) cc_final: 0.8160 (mmt180) REVERT: C 199 ARG cc_start: 0.8329 (mtt-85) cc_final: 0.8036 (mtm110) REVERT: C 296 GLU cc_start: 0.8148 (tt0) cc_final: 0.7564 (tp30) REVERT: C 379 MET cc_start: 0.7398 (mtm) cc_final: 0.7146 (mtt) REVERT: C 459 MET cc_start: 0.7795 (mmm) cc_final: 0.7283 (mtm) outliers start: 35 outliers final: 22 residues processed: 161 average time/residue: 1.4548 time to fit residues: 254.5137 Evaluate side-chains 153 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 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 34 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 532 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 23 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 45 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.136990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.111710 restraints weight = 12585.945| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.41 r_work: 0.3057 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12850 Z= 0.147 Angle : 0.569 6.570 17466 Z= 0.286 Chirality : 0.043 0.128 1957 Planarity : 0.004 0.045 2229 Dihedral : 5.770 53.318 1878 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.61 % Allowed : 13.80 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.20), residues: 1590 helix: 1.53 (0.21), residues: 612 sheet: 0.18 (0.33), residues: 216 loop : -0.66 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 74 HIS 0.003 0.001 HIS C 140 PHE 0.017 0.002 PHE A 218 TYR 0.013 0.002 TYR C 152 ARG 0.002 0.000 ARG C 104 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 1) link_NAG-ASN : angle 1.80903 ( 3) link_BETA1-4 : bond 0.00635 ( 6) link_BETA1-4 : angle 1.34131 ( 18) hydrogen bonds : bond 0.04096 ( 552) hydrogen bonds : angle 5.33237 ( 1584) SS BOND : bond 0.00286 ( 6) SS BOND : angle 2.21262 ( 12) covalent geometry : bond 0.00364 (12837) covalent geometry : angle 0.56409 (17433) *********************** 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 169 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 1.170 Fit side-chains REVERT: A 106 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7403 (pm20) REVERT: A 111 LYS cc_start: 0.8191 (mtmm) cc_final: 0.7896 (mtmp) REVERT: A 199 ARG cc_start: 0.8402 (mtt-85) cc_final: 0.8170 (mtp180) REVERT: A 326 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8152 (mmt) REVERT: A 376 LYS cc_start: 0.7458 (mttp) cc_final: 0.7008 (tppt) REVERT: A 379 MET cc_start: 0.7461 (mtp) cc_final: 0.7192 (mtt) REVERT: B 95 GLN cc_start: 0.8518 (tt0) cc_final: 0.8135 (tt0) REVERT: B 106 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7555 (pm20) REVERT: B 111 LYS cc_start: 0.8313 (mtmm) cc_final: 0.7916 (mtmt) REVERT: B 132 ARG cc_start: 0.8285 (mmm160) cc_final: 0.7963 (mmt180) REVERT: B 267 GLN cc_start: 0.7856 (tp40) cc_final: 0.7507 (mt0) REVERT: B 275 LYS cc_start: 0.7578 (mmtp) cc_final: 0.7248 (mtmt) REVERT: B 296 GLU cc_start: 0.8164 (tt0) cc_final: 0.7927 (tp30) REVERT: B 326 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8097 (mmt) REVERT: B 363 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5526 (mp) REVERT: B 364 MET cc_start: 0.7611 (mtm) cc_final: 0.7347 (mtp) REVERT: B 457 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8375 (p) REVERT: B 487 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7189 (mm-30) REVERT: C 41 GLU cc_start: 0.8477 (tt0) cc_final: 0.7926 (mp0) REVERT: C 106 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7548 (pm20) REVERT: C 111 LYS cc_start: 0.8280 (mtmm) cc_final: 0.7992 (mtmm) REVERT: C 132 ARG cc_start: 0.8488 (mmm160) cc_final: 0.8231 (mmt180) REVERT: C 199 ARG cc_start: 0.8335 (mtt-85) cc_final: 0.8110 (mtm110) REVERT: C 296 GLU cc_start: 0.8160 (tt0) cc_final: 0.7564 (tp30) REVERT: C 459 MET cc_start: 0.7809 (mmm) cc_final: 0.7284 (mtm) outliers start: 35 outliers final: 19 residues processed: 161 average time/residue: 1.4143 time to fit residues: 245.8949 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 : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 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 326 MET Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 532 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 76 optimal weight: 0.0980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0060 chunk 43 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 36 optimal weight: 0.0270 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.139487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.116224 restraints weight = 12920.246| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.11 r_work: 0.3106 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12850 Z= 0.086 Angle : 0.488 5.230 17466 Z= 0.244 Chirality : 0.040 0.129 1957 Planarity : 0.004 0.046 2229 Dihedral : 5.319 52.983 1878 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.86 % Allowed : 14.91 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1590 helix: 1.92 (0.22), residues: 612 sheet: 0.06 (0.31), residues: 246 loop : -0.43 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 547 HIS 0.001 0.000 HIS B 342 PHE 0.017 0.001 PHE A 218 TYR 0.007 0.001 TYR B 403 ARG 0.001 0.000 ARG A 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00085 ( 1) link_NAG-ASN : angle 1.48483 ( 3) link_BETA1-4 : bond 0.00564 ( 6) link_BETA1-4 : angle 1.22986 ( 18) hydrogen bonds : bond 0.03013 ( 552) hydrogen bonds : angle 5.08635 ( 1584) SS BOND : bond 0.00162 ( 6) SS BOND : angle 1.69781 ( 12) covalent geometry : bond 0.00192 (12837) covalent geometry : angle 0.48470 (17433) *********************** 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 169 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.431 Fit side-chains revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7382 (pm20) REVERT: A 111 LYS cc_start: 0.8122 (mtmm) cc_final: 0.7814 (mtmp) REVERT: A 199 ARG cc_start: 0.8389 (mtt-85) cc_final: 0.8137 (mtp180) REVERT: A 296 GLU cc_start: 0.8131 (tt0) cc_final: 0.7614 (tp30) REVERT: A 326 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.7574 (mmt) REVERT: A 376 LYS cc_start: 0.7389 (mttp) cc_final: 0.6896 (tppt) REVERT: B 69 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8015 (mt0) REVERT: B 95 GLN cc_start: 0.8502 (tt0) cc_final: 0.8123 (tt0) REVERT: B 106 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7573 (pm20) REVERT: B 111 LYS cc_start: 0.8242 (mtmm) cc_final: 0.7863 (mtmt) REVERT: B 132 ARG cc_start: 0.8254 (mmm160) cc_final: 0.7979 (mmt180) REVERT: B 296 GLU cc_start: 0.8139 (tt0) cc_final: 0.7797 (tp30) REVERT: B 363 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5417 (mp) REVERT: B 364 MET cc_start: 0.7552 (mtm) cc_final: 0.7342 (mtp) REVERT: C 41 GLU cc_start: 0.8453 (tt0) cc_final: 0.7976 (mp0) REVERT: C 106 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7560 (pm20) REVERT: C 111 LYS cc_start: 0.8166 (mtmm) cc_final: 0.7846 (mtmm) REVERT: C 132 ARG cc_start: 0.8432 (mmm160) cc_final: 0.8197 (mmt180) REVERT: C 199 ARG cc_start: 0.8330 (mtt-85) cc_final: 0.8122 (mtm110) REVERT: C 296 GLU cc_start: 0.8152 (tt0) cc_final: 0.7539 (tp30) REVERT: C 398 GLU cc_start: 0.6944 (tp30) cc_final: 0.6308 (tt0) REVERT: C 459 MET cc_start: 0.7723 (mmm) cc_final: 0.7290 (mtm) REVERT: C 487 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7851 (tp30) outliers start: 25 outliers final: 10 residues processed: 162 average time/residue: 1.4642 time to fit residues: 256.1778 Evaluate side-chains 146 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 1.395 ------------------------------------------------------------------------------- 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 483 GLU Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 363 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 66 optimal weight: 0.9980 chunk 118 optimal weight: 0.0670 chunk 9 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 75 optimal weight: 0.0020 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 36 optimal weight: 0.0770 chunk 86 optimal weight: 0.4980 overall best weight: 0.2884 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.140887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.118373 restraints weight = 12720.471| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.06 r_work: 0.3124 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12850 Z= 0.086 Angle : 0.491 5.020 17466 Z= 0.245 Chirality : 0.040 0.129 1957 Planarity : 0.004 0.045 2229 Dihedral : 5.236 52.896 1875 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.86 % Allowed : 14.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.21), residues: 1590 helix: 1.99 (0.22), residues: 615 sheet: 0.12 (0.31), residues: 246 loop : -0.38 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 547 HIS 0.001 0.000 HIS C 140 PHE 0.018 0.001 PHE C 218 TYR 0.007 0.001 TYR B 403 ARG 0.002 0.000 ARG C 505 Details of bonding type rmsd link_NAG-ASN : bond 0.00057 ( 1) link_NAG-ASN : angle 1.37120 ( 3) link_BETA1-4 : bond 0.00573 ( 6) link_BETA1-4 : angle 1.29396 ( 18) hydrogen bonds : bond 0.02965 ( 552) hydrogen bonds : angle 5.02175 ( 1584) SS BOND : bond 0.00238 ( 6) SS BOND : angle 1.95397 ( 12) covalent geometry : bond 0.00194 (12837) covalent geometry : angle 0.48629 (17433) *********************** 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 165 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.469 Fit side-chains REVERT: A 106 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7386 (pm20) REVERT: A 111 LYS cc_start: 0.8079 (mtmm) cc_final: 0.7789 (mtmm) REVERT: A 296 GLU cc_start: 0.8085 (tt0) cc_final: 0.7579 (tp30) REVERT: A 326 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.7505 (mmt) REVERT: A 376 LYS cc_start: 0.7484 (mttp) cc_final: 0.7009 (tppt) REVERT: A 487 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7529 (tp30) REVERT: B 69 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8001 (mt0) REVERT: B 95 GLN cc_start: 0.8452 (tt0) cc_final: 0.8070 (tt0) REVERT: B 106 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7578 (pm20) REVERT: B 111 LYS cc_start: 0.8212 (mtmm) cc_final: 0.7887 (mtmt) REVERT: B 132 ARG cc_start: 0.8263 (mmm160) cc_final: 0.8006 (mmt180) REVERT: B 296 GLU cc_start: 0.8131 (tt0) cc_final: 0.7793 (tp30) REVERT: B 326 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8372 (mmm) REVERT: B 363 LEU cc_start: 0.5748 (OUTLIER) cc_final: 0.5309 (mp) REVERT: B 364 MET cc_start: 0.7521 (mtm) cc_final: 0.7314 (mtp) REVERT: B 457 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.8242 (p) REVERT: C 41 GLU cc_start: 0.8432 (tt0) cc_final: 0.7986 (mp0) REVERT: C 106 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7524 (pm20) REVERT: C 111 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7813 (mtmm) REVERT: C 132 ARG cc_start: 0.8434 (mmm160) cc_final: 0.8212 (mmt180) REVERT: C 296 GLU cc_start: 0.8125 (tt0) cc_final: 0.7501 (tp30) REVERT: C 398 GLU cc_start: 0.6939 (tp30) cc_final: 0.6340 (tt0) REVERT: C 459 MET cc_start: 0.7659 (mmm) cc_final: 0.7263 (mtm) REVERT: C 487 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7880 (tp30) outliers start: 25 outliers final: 7 residues processed: 157 average time/residue: 1.5984 time to fit residues: 270.5114 Evaluate side-chains 143 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain B residue 69 GLN 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 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 363 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 93 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 0.0040 chunk 132 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 152 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 76 optimal weight: 0.0370 chunk 140 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 overall best weight: 0.4870 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.141504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.118078 restraints weight = 12575.115| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.11 r_work: 0.3111 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12850 Z= 0.096 Angle : 0.524 10.600 17466 Z= 0.262 Chirality : 0.041 0.127 1957 Planarity : 0.004 0.045 2229 Dihedral : 5.260 53.000 1875 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.49 % Allowed : 15.44 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1590 helix: 1.97 (0.22), residues: 615 sheet: 0.16 (0.31), residues: 246 loop : -0.39 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 547 HIS 0.002 0.001 HIS C 184 PHE 0.018 0.001 PHE C 218 TYR 0.008 0.001 TYR A 447 ARG 0.003 0.000 ARG A 199 Details of bonding type rmsd link_NAG-ASN : bond 0.00057 ( 1) link_NAG-ASN : angle 1.37401 ( 3) link_BETA1-4 : bond 0.00581 ( 6) link_BETA1-4 : angle 1.29972 ( 18) hydrogen bonds : bond 0.03111 ( 552) hydrogen bonds : angle 5.01618 ( 1584) SS BOND : bond 0.00322 ( 6) SS BOND : angle 3.13397 ( 12) covalent geometry : bond 0.00226 (12837) covalent geometry : angle 0.51555 (17433) *********************** 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 152 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.530 Fit side-chains revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7375 (pm20) REVERT: A 111 LYS cc_start: 0.8095 (mtmm) cc_final: 0.7789 (mtmm) REVERT: A 296 GLU cc_start: 0.8064 (tt0) cc_final: 0.7564 (tp30) REVERT: A 326 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.7610 (mmt) REVERT: A 352 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.7446 (ttmt) REVERT: A 376 LYS cc_start: 0.7565 (mttp) cc_final: 0.7079 (tppt) REVERT: A 419 ASP cc_start: 0.7516 (m-30) cc_final: 0.7209 (m-30) REVERT: A 487 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7542 (tp30) REVERT: B 69 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8004 (mt0) REVERT: B 95 GLN cc_start: 0.8470 (tt0) cc_final: 0.8090 (tt0) REVERT: B 106 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7583 (pm20) REVERT: B 111 LYS cc_start: 0.8228 (mtmm) cc_final: 0.7904 (mtmt) REVERT: B 132 ARG cc_start: 0.8283 (mmm160) cc_final: 0.8030 (mmt180) REVERT: B 296 GLU cc_start: 0.8150 (tt0) cc_final: 0.7899 (tp30) REVERT: B 326 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8375 (mmm) REVERT: B 363 LEU cc_start: 0.5504 (OUTLIER) cc_final: 0.5130 (mp) REVERT: B 398 GLU cc_start: 0.6923 (tp30) cc_final: 0.6419 (tt0) REVERT: B 457 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8248 (p) REVERT: C 41 GLU cc_start: 0.8435 (tt0) cc_final: 0.7980 (mp0) REVERT: C 106 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7511 (pm20) REVERT: C 111 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7816 (mtmm) REVERT: C 132 ARG cc_start: 0.8422 (mmm160) cc_final: 0.8204 (mmt180) REVERT: C 296 GLU cc_start: 0.8146 (tt0) cc_final: 0.7513 (tp30) REVERT: C 398 GLU cc_start: 0.6937 (tp30) cc_final: 0.6330 (tt0) REVERT: C 459 MET cc_start: 0.7644 (mmm) cc_final: 0.7253 (mtm) REVERT: C 487 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7786 (tp30) outliers start: 20 outliers final: 9 residues processed: 146 average time/residue: 1.5665 time to fit residues: 245.8329 Evaluate side-chains 144 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.462 ------------------------------------------------------------------------------- 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 463 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 69 GLN 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 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 285 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 33 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 151 optimal weight: 0.1980 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.137061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.113469 restraints weight = 12654.901| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.12 r_work: 0.3047 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12850 Z= 0.165 Angle : 0.600 10.227 17466 Z= 0.303 Chirality : 0.045 0.130 1957 Planarity : 0.004 0.046 2229 Dihedral : 5.562 53.801 1875 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.49 % Allowed : 15.59 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1590 helix: 1.70 (0.21), residues: 612 sheet: 0.31 (0.33), residues: 216 loop : -0.60 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 74 HIS 0.004 0.001 HIS B 140 PHE 0.019 0.002 PHE C 218 TYR 0.014 0.002 TYR B 152 ARG 0.005 0.000 ARG C 505 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 1) link_NAG-ASN : angle 1.68792 ( 3) link_BETA1-4 : bond 0.00646 ( 6) link_BETA1-4 : angle 1.33415 ( 18) hydrogen bonds : bond 0.04093 ( 552) hydrogen bonds : angle 5.20567 ( 1584) SS BOND : bond 0.00275 ( 6) SS BOND : angle 3.66460 ( 12) covalent geometry : bond 0.00413 (12837) covalent geometry : angle 0.59065 (17433) *********************** 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 148 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.466 Fit side-chains REVERT: A 106 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7368 (pm20) REVERT: A 111 LYS cc_start: 0.8120 (mtmm) cc_final: 0.7843 (mtmp) REVERT: A 326 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8108 (mmt) REVERT: A 352 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.7530 (ttmt) REVERT: A 376 LYS cc_start: 0.7588 (mttp) cc_final: 0.7107 (mmtt) REVERT: B 69 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8050 (mt0) REVERT: B 95 GLN cc_start: 0.8521 (tt0) cc_final: 0.8146 (tt0) REVERT: B 106 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7595 (pm20) REVERT: B 111 LYS cc_start: 0.8313 (mtmm) cc_final: 0.7930 (mtmt) REVERT: B 132 ARG cc_start: 0.8350 (mmm160) cc_final: 0.8087 (mmt180) REVERT: B 296 GLU cc_start: 0.8219 (tt0) cc_final: 0.7832 (tp30) REVERT: B 363 LEU cc_start: 0.5479 (OUTLIER) cc_final: 0.5180 (mp) REVERT: B 457 SER cc_start: 0.8556 (OUTLIER) cc_final: 0.8279 (p) REVERT: C 41 GLU cc_start: 0.8457 (tt0) cc_final: 0.7918 (mp0) REVERT: C 106 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7522 (pm20) REVERT: C 111 LYS cc_start: 0.8254 (mtmm) cc_final: 0.7991 (mtmm) REVERT: C 132 ARG cc_start: 0.8457 (mmm160) cc_final: 0.8229 (mmt180) REVERT: C 296 GLU cc_start: 0.8194 (tt0) cc_final: 0.7579 (tp30) REVERT: C 398 GLU cc_start: 0.7012 (tp30) cc_final: 0.6349 (tt0) REVERT: C 459 MET cc_start: 0.7779 (mmm) cc_final: 0.7375 (mtm) outliers start: 20 outliers final: 9 residues processed: 143 average time/residue: 1.5614 time to fit residues: 240.0338 Evaluate side-chains 142 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 2.010 ------------------------------------------------------------------------------- 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 463 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 69 GLN 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 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 285 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 128 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 144 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 140 optimal weight: 0.0670 chunk 25 optimal weight: 0.4980 chunk 104 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 154 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.140417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.117137 restraints weight = 12531.252| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.10 r_work: 0.3090 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12850 Z= 0.098 Angle : 0.519 7.989 17466 Z= 0.261 Chirality : 0.041 0.128 1957 Planarity : 0.004 0.046 2229 Dihedral : 5.361 53.351 1875 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.27 % Allowed : 16.03 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.21), residues: 1590 helix: 1.88 (0.21), residues: 612 sheet: 0.15 (0.31), residues: 246 loop : -0.46 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 547 HIS 0.003 0.001 HIS C 140 PHE 0.019 0.001 PHE C 218 TYR 0.009 0.001 TYR B 152 ARG 0.003 0.000 ARG A 199 Details of bonding type rmsd link_NAG-ASN : bond 0.00111 ( 1) link_NAG-ASN : angle 1.51614 ( 3) link_BETA1-4 : bond 0.00599 ( 6) link_BETA1-4 : angle 1.20960 ( 18) hydrogen bonds : bond 0.03261 ( 552) hydrogen bonds : angle 5.05188 ( 1584) SS BOND : bond 0.00165 ( 6) SS BOND : angle 2.61543 ( 12) covalent geometry : bond 0.00233 (12837) covalent geometry : angle 0.51302 (17433) ********************** 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 151 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.617 Fit side-chains REVERT: A 106 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7298 (pm20) REVERT: A 111 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7835 (mtmm) REVERT: A 296 GLU cc_start: 0.8080 (tt0) cc_final: 0.7577 (tp30) REVERT: A 326 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.7668 (mmt) REVERT: A 352 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8344 (tptt) REVERT: A 376 LYS cc_start: 0.7589 (mttp) cc_final: 0.7112 (mmtt) REVERT: A 419 ASP cc_start: 0.7485 (m-30) cc_final: 0.7174 (m-30) REVERT: A 459 MET cc_start: 0.8079 (mpp) cc_final: 0.7796 (mtt) REVERT: A 487 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7581 (tp30) REVERT: B 69 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8008 (mt0) REVERT: B 95 GLN cc_start: 0.8488 (tt0) cc_final: 0.8104 (tt0) REVERT: B 106 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7582 (pm20) REVERT: B 111 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7899 (mtmt) REVERT: B 132 ARG cc_start: 0.8291 (mmm160) cc_final: 0.8051 (mmt180) REVERT: B 296 GLU cc_start: 0.8144 (tt0) cc_final: 0.7805 (tp30) REVERT: B 326 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.7303 (mmp) REVERT: B 398 GLU cc_start: 0.6911 (tp30) cc_final: 0.6397 (tt0) REVERT: B 457 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.8245 (p) REVERT: C 41 GLU cc_start: 0.8398 (tt0) cc_final: 0.7941 (mp0) REVERT: C 106 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7522 (pm20) REVERT: C 111 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7957 (mtmm) REVERT: C 132 ARG cc_start: 0.8408 (mmm160) cc_final: 0.8187 (mmt180) REVERT: C 296 GLU cc_start: 0.8147 (tt0) cc_final: 0.7532 (tp30) REVERT: C 398 GLU cc_start: 0.6980 (tp30) cc_final: 0.6370 (tt0) REVERT: C 459 MET cc_start: 0.7727 (mmm) cc_final: 0.7326 (mtm) outliers start: 17 outliers final: 8 residues processed: 147 average time/residue: 1.8164 time to fit residues: 288.9477 Evaluate side-chains 143 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.853 ------------------------------------------------------------------------------- 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 463 THR Chi-restraints excluded: chain B residue 69 GLN 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 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 285 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 35 optimal weight: 7.9990 chunk 146 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.139981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.114524 restraints weight = 12643.449| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.41 r_work: 0.3067 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12850 Z= 0.113 Angle : 0.538 7.891 17466 Z= 0.270 Chirality : 0.042 0.129 1957 Planarity : 0.004 0.045 2229 Dihedral : 5.357 53.435 1875 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.19 % Allowed : 16.03 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1590 helix: 1.86 (0.21), residues: 612 sheet: 0.13 (0.31), residues: 246 loop : -0.47 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 357 HIS 0.002 0.001 HIS B 140 PHE 0.018 0.001 PHE C 218 TYR 0.010 0.001 TYR B 152 ARG 0.003 0.000 ARG A 199 Details of bonding type rmsd link_NAG-ASN : bond 0.00123 ( 1) link_NAG-ASN : angle 1.54928 ( 3) link_BETA1-4 : bond 0.00608 ( 6) link_BETA1-4 : angle 1.27002 ( 18) hydrogen bonds : bond 0.03483 ( 552) hydrogen bonds : angle 5.08189 ( 1584) SS BOND : bond 0.00168 ( 6) SS BOND : angle 3.09202 ( 12) covalent geometry : bond 0.00274 (12837) covalent geometry : angle 0.53061 (17433) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10449.15 seconds wall clock time: 187 minutes 14.57 seconds (11234.57 seconds total)