Starting phenix.real_space_refine on Wed Apr 30 16:14:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ave_7009/04_2025/6ave_7009.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ave_7009/04_2025/6ave_7009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ave_7009/04_2025/6ave_7009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ave_7009/04_2025/6ave_7009.map" model { file = "/net/cci-nas-00/data/ceres_data/6ave_7009/04_2025/6ave_7009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ave_7009/04_2025/6ave_7009.cif" } resolution = 3.7 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= 0.031 sd= 1.102 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 81 5.16 5 C 6204 2.51 5 N 1581 2.21 5 O 1791 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9657 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3191 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 403} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 135 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: C, B Time building chain proxies: 5.98, per 1000 atoms: 0.62 Number of scatterers: 9657 At special positions: 0 Unit cell: (95.68, 98.8, 128.96, 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 81 16.00 O 1791 8.00 N 1581 7.00 C 6204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 195 " distance=2.01 Simple disulfide: pdb=" SG CYS A 173 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 366 " distance=2.03 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 195 " distance=2.01 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 195 " distance=2.01 Simple disulfide: pdb=" SG CYS C 173 " - pdb=" SG CYS C 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 173 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 366 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 366 " distance=2.03 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 362 " distance=2.03 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 362 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 336 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 336 " 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 NAG-ASN " NAG A 601 " - " ASN A 394 " " NAG A 602 " - " ASN A 367 " " NAG B 601 " - " ASN B 394 " " NAG B 602 " - " ASN B 367 " " NAG C 601 " - " ASN C 394 " " NAG C 602 " - " ASN C 367 " Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2382 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 40.2% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 41 through 70 Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 132 through 143 removed outlier: 3.712A pdb=" N LEU A 139 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.733A pdb=" N PHE A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.522A pdb=" N TYR A 230 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 305 through 323 removed outlier: 3.895A pdb=" N ASN A 323 " --> pdb=" O VAL A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.728A pdb=" N LYS A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 355 Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.814A pdb=" N CYS A 360 " --> pdb=" O ASN A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 394 removed outlier: 3.722A pdb=" N LEU A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 426 through 441 Processing helix chain 'A' and resid 445 through 464 removed outlier: 3.821A pdb=" N LYS A 461 " --> pdb=" O TYR A 457 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N HIS A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 70 Processing helix chain 'B' and resid 105 through 113 Processing helix chain 'B' and resid 132 through 143 removed outlier: 3.712A pdb=" N LEU B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.734A pdb=" N PHE B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.521A pdb=" N TYR B 230 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 305 through 323 removed outlier: 3.895A pdb=" N ASN B 323 " --> pdb=" O VAL B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.726A pdb=" N LYS B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 355 Processing helix chain 'B' and resid 356 through 360 removed outlier: 3.815A pdb=" N CYS B 360 " --> pdb=" O ASN B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 394 removed outlier: 3.721A pdb=" N LEU B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 426 through 441 Processing helix chain 'B' and resid 445 through 464 removed outlier: 3.822A pdb=" N LYS B 461 " --> pdb=" O TYR B 457 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N HIS B 462 " --> pdb=" O GLU B 458 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 70 Processing helix chain 'C' and resid 105 through 113 Processing helix chain 'C' and resid 132 through 143 removed outlier: 3.711A pdb=" N LEU C 139 " --> pdb=" O GLN C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 removed outlier: 3.734A pdb=" N PHE C 158 " --> pdb=" O ASN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 183 No H-bonds generated for 'chain 'C' and resid 181 through 183' Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.522A pdb=" N TYR C 230 " --> pdb=" O GLN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 305 through 323 removed outlier: 3.896A pdb=" N ASN C 323 " --> pdb=" O VAL C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 344 removed outlier: 3.727A pdb=" N LYS C 342 " --> pdb=" O PRO C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 355 Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.814A pdb=" N CYS C 360 " --> pdb=" O ASN C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 394 removed outlier: 3.722A pdb=" N LEU C 389 " --> pdb=" O SER C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 426 through 441 Processing helix chain 'C' and resid 445 through 464 removed outlier: 3.822A pdb=" N LYS C 461 " --> pdb=" O TYR C 457 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N HIS C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 82 removed outlier: 7.397A pdb=" N ASN A 415 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU A 278 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE A 270 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A 172 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASP A 224 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU A 170 " --> pdb=" O ASP A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 82 removed outlier: 7.397A pdb=" N ASN A 415 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU A 278 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 removed outlier: 3.670A pdb=" N LEU A 86 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 189 removed outlier: 7.102A pdb=" N LYS A 194 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASN A 95 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 82 removed outlier: 7.397A pdb=" N ASN B 415 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU B 278 " --> pdb=" O ASN B 415 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE B 270 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 172 " --> pdb=" O MET B 222 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASP B 224 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU B 170 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 74 through 82 removed outlier: 7.397A pdb=" N ASN B 415 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU B 278 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 86 through 87 removed outlier: 3.670A pdb=" N LEU B 86 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 185 through 189 removed outlier: 7.102A pdb=" N LYS B 194 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ASN B 95 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 74 through 82 removed outlier: 7.397A pdb=" N ASN C 415 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU C 278 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE C 270 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER C 172 " --> pdb=" O MET C 222 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASP C 224 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU C 170 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 74 through 82 removed outlier: 7.397A pdb=" N ASN C 415 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU C 278 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 86 through 87 removed outlier: 3.670A pdb=" N LEU C 86 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 185 through 189 removed outlier: 7.102A pdb=" N LYS C 194 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ASN C 95 " --> pdb=" O LYS C 194 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1515 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3120 1.35 - 1.47: 2594 1.47 - 1.60: 4063 1.60 - 1.73: 0 1.73 - 1.85: 111 Bond restraints: 9888 Sorted by residual: bond pdb=" CG1 ILE C 259 " pdb=" CD1 ILE C 259 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.76e+00 bond pdb=" CG1 ILE A 259 " pdb=" CD1 ILE A 259 " ideal model delta sigma weight residual 1.513 1.429 0.084 3.90e-02 6.57e+02 4.68e+00 bond pdb=" CG1 ILE B 259 " pdb=" CD1 ILE B 259 " ideal model delta sigma weight residual 1.513 1.429 0.084 3.90e-02 6.57e+02 4.66e+00 bond pdb=" C ASN C 367 " pdb=" N VAL C 368 " ideal model delta sigma weight residual 1.329 1.286 0.044 2.19e-02 2.09e+03 3.97e+00 bond pdb=" C ASN A 367 " pdb=" N VAL A 368 " ideal model delta sigma weight residual 1.329 1.287 0.043 2.19e-02 2.09e+03 3.78e+00 ... (remaining 9883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 12845 1.86 - 3.72: 523 3.72 - 5.58: 72 5.58 - 7.44: 12 7.44 - 9.30: 6 Bond angle restraints: 13458 Sorted by residual: angle pdb=" C ILE B 380 " pdb=" N PRO B 381 " pdb=" CA PRO B 381 " ideal model delta sigma weight residual 127.00 135.24 -8.24 2.40e+00 1.74e-01 1.18e+01 angle pdb=" C ILE C 380 " pdb=" N PRO C 381 " pdb=" CA PRO C 381 " ideal model delta sigma weight residual 127.00 135.24 -8.24 2.40e+00 1.74e-01 1.18e+01 angle pdb=" C ILE A 380 " pdb=" N PRO A 381 " pdb=" CA PRO A 381 " ideal model delta sigma weight residual 127.00 135.21 -8.21 2.40e+00 1.74e-01 1.17e+01 angle pdb=" C ILE C 380 " pdb=" N PRO C 381 " pdb=" CD PRO C 381 " ideal model delta sigma weight residual 120.60 113.64 6.96 2.20e+00 2.07e-01 1.00e+01 angle pdb=" C ILE B 380 " pdb=" N PRO B 381 " pdb=" CD PRO B 381 " ideal model delta sigma weight residual 120.60 113.64 6.96 2.20e+00 2.07e-01 1.00e+01 ... (remaining 13453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 5680 15.16 - 30.32: 236 30.32 - 45.48: 45 45.48 - 60.64: 18 60.64 - 75.80: 6 Dihedral angle restraints: 5985 sinusoidal: 2268 harmonic: 3717 Sorted by residual: dihedral pdb=" CA THR B 337 " pdb=" C THR B 337 " pdb=" N PRO B 338 " pdb=" CA PRO B 338 " ideal model delta harmonic sigma weight residual 180.00 -151.40 -28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA THR C 337 " pdb=" C THR C 337 " pdb=" N PRO C 338 " pdb=" CA PRO C 338 " ideal model delta harmonic sigma weight residual -180.00 -151.42 -28.58 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA THR A 337 " pdb=" C THR A 337 " pdb=" N PRO A 338 " pdb=" CA PRO A 338 " ideal model delta harmonic sigma weight residual -180.00 -151.44 -28.56 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 5982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 1500 0.189 - 0.378: 9 0.378 - 0.567: 0 0.567 - 0.756: 0 0.756 - 0.945: 3 Chirality restraints: 1512 Sorted by residual: chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 367 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.23e+01 chirality pdb=" C1 NAG B 602 " pdb=" ND2 ASN B 367 " pdb=" C2 NAG B 602 " pdb=" O5 NAG B 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.20e+01 chirality pdb=" C1 NAG C 602 " pdb=" ND2 ASN C 367 " pdb=" C2 NAG C 602 " pdb=" O5 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.18e+01 ... (remaining 1509 not shown) Planarity restraints: 1755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 107 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C ASN C 107 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN C 107 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP C 108 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 107 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.26e+00 pdb=" C ASN B 107 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN B 107 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP B 108 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 107 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C ASN A 107 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN A 107 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP A 108 " -0.013 2.00e-02 2.50e+03 ... (remaining 1752 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3161 2.82 - 3.34: 8653 3.34 - 3.86: 15709 3.86 - 4.38: 18193 4.38 - 4.90: 30272 Nonbonded interactions: 75988 Sorted by model distance: nonbonded pdb=" OG1 THR C 215 " pdb=" OD2 ASP C 408 " model vdw 2.301 3.040 nonbonded pdb=" OG1 THR B 215 " pdb=" OD2 ASP B 408 " model vdw 2.302 3.040 nonbonded pdb=" OG1 THR A 215 " pdb=" OD2 ASP A 408 " model vdw 2.302 3.040 nonbonded pdb=" NE2 HIS B 111 " pdb=" O LYS B 151 " model vdw 2.308 3.120 nonbonded pdb=" NE2 HIS C 111 " pdb=" O LYS C 151 " model vdw 2.308 3.120 ... (remaining 75983 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.210 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 9915 Z= 0.376 Angle : 0.927 13.827 13518 Z= 0.485 Chirality : 0.068 0.945 1512 Planarity : 0.005 0.040 1749 Dihedral : 9.624 75.799 3540 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -3.23 (0.20), residues: 1266 helix: -2.76 (0.17), residues: 432 sheet: -1.68 (0.28), residues: 279 loop : -1.67 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 47 HIS 0.010 0.002 HIS C 251 PHE 0.023 0.003 PHE B 453 TYR 0.030 0.003 TYR C 393 ARG 0.008 0.001 ARG B 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00781 ( 6) link_NAG-ASN : angle 7.75319 ( 18) hydrogen bonds : bond 0.12258 ( 484) hydrogen bonds : angle 8.77609 ( 1515) SS BOND : bond 0.00706 ( 21) SS BOND : angle 2.05867 ( 42) covalent geometry : bond 0.00791 ( 9888) covalent geometry : angle 0.87754 (13458) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8838 (t80) cc_final: 0.8329 (t80) REVERT: A 198 PHE cc_start: 0.8663 (t80) cc_final: 0.8453 (t80) REVERT: A 217 ASN cc_start: 0.7848 (m110) cc_final: 0.6891 (t0) REVERT: A 247 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8240 (ttmm) REVERT: A 249 GLN cc_start: 0.7706 (tm-30) cc_final: 0.6784 (tm-30) REVERT: A 278 GLU cc_start: 0.8390 (tt0) cc_final: 0.7708 (tt0) REVERT: A 309 CYS cc_start: 0.6570 (t) cc_final: 0.6331 (t) REVERT: A 323 ASN cc_start: 0.8097 (m-40) cc_final: 0.7864 (m110) REVERT: A 341 TYR cc_start: 0.7407 (m-10) cc_final: 0.7178 (m-10) REVERT: A 350 ASP cc_start: 0.8450 (m-30) cc_final: 0.8023 (m-30) REVERT: A 379 LYS cc_start: 0.8289 (ttpt) cc_final: 0.7976 (tptt) REVERT: A 420 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7478 (mt-10) REVERT: A 454 ASP cc_start: 0.8266 (m-30) cc_final: 0.7878 (m-30) REVERT: B 217 ASN cc_start: 0.7801 (m110) cc_final: 0.6800 (t0) REVERT: B 249 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7520 (tt0) REVERT: B 262 LEU cc_start: 0.9124 (mt) cc_final: 0.8839 (mp) REVERT: B 278 GLU cc_start: 0.8303 (tt0) cc_final: 0.7838 (tt0) REVERT: B 280 ARG cc_start: 0.8386 (mtt180) cc_final: 0.8114 (mtt180) REVERT: B 309 CYS cc_start: 0.6657 (t) cc_final: 0.6456 (t) REVERT: B 350 ASP cc_start: 0.8312 (m-30) cc_final: 0.7897 (m-30) REVERT: B 420 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7388 (mt-10) REVERT: C 61 VAL cc_start: 0.8623 (m) cc_final: 0.8221 (p) REVERT: C 220 GLU cc_start: 0.7506 (tt0) cc_final: 0.7157 (tt0) REVERT: C 247 LYS cc_start: 0.8589 (ttmm) cc_final: 0.8088 (ttmm) REVERT: C 278 GLU cc_start: 0.8318 (tt0) cc_final: 0.7666 (tt0) REVERT: C 280 ARG cc_start: 0.8386 (mtt180) cc_final: 0.7560 (mtt180) REVERT: C 309 CYS cc_start: 0.6709 (t) cc_final: 0.6445 (t) REVERT: C 341 TYR cc_start: 0.7366 (m-10) cc_final: 0.7072 (m-10) REVERT: C 350 ASP cc_start: 0.8432 (m-30) cc_final: 0.8061 (m-30) REVERT: C 373 LYS cc_start: 0.7872 (pttm) cc_final: 0.7580 (mttt) REVERT: C 379 LYS cc_start: 0.8124 (ttpt) cc_final: 0.7749 (tptp) REVERT: C 403 ASN cc_start: 0.8128 (m-40) cc_final: 0.7447 (m110) REVERT: C 420 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7335 (mt-10) REVERT: C 437 GLN cc_start: 0.8921 (mt0) cc_final: 0.8575 (mt0) outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.2560 time to fit residues: 146.0380 Evaluate side-chains 246 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 98 optimal weight: 0.0470 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 GLN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 403 ASN C 249 GLN C 277 GLN ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.161166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.138034 restraints weight = 16369.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.142132 restraints weight = 9283.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.144927 restraints weight = 6230.943| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9915 Z= 0.180 Angle : 0.730 11.156 13518 Z= 0.372 Chirality : 0.048 0.432 1512 Planarity : 0.005 0.036 1749 Dihedral : 6.451 41.029 1500 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.64 % Allowed : 14.58 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.59 (0.22), residues: 1266 helix: -0.64 (0.23), residues: 441 sheet: -1.46 (0.29), residues: 267 loop : -1.01 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 47 HIS 0.007 0.002 HIS C 328 PHE 0.024 0.002 PHE B 270 TYR 0.014 0.002 TYR C 230 ARG 0.009 0.001 ARG B 370 Details of bonding type rmsd link_NAG-ASN : bond 0.00833 ( 6) link_NAG-ASN : angle 5.41066 ( 18) hydrogen bonds : bond 0.03946 ( 484) hydrogen bonds : angle 5.80435 ( 1515) SS BOND : bond 0.00754 ( 21) SS BOND : angle 2.60705 ( 42) covalent geometry : bond 0.00376 ( 9888) covalent geometry : angle 0.68928 (13458) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 280 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8771 (t80) cc_final: 0.8315 (t80) REVERT: A 108 ASP cc_start: 0.6687 (m-30) cc_final: 0.6430 (m-30) REVERT: A 217 ASN cc_start: 0.7590 (m110) cc_final: 0.6899 (t0) REVERT: A 249 GLN cc_start: 0.8425 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 280 ARG cc_start: 0.8559 (mtt180) cc_final: 0.8185 (mtt180) REVERT: A 309 CYS cc_start: 0.6672 (t) cc_final: 0.6395 (t) REVERT: A 430 LEU cc_start: 0.9117 (tp) cc_final: 0.8808 (tt) REVERT: B 217 ASN cc_start: 0.7331 (m110) cc_final: 0.6720 (t0) REVERT: B 242 PHE cc_start: 0.8637 (m-80) cc_final: 0.8431 (m-80) REVERT: B 249 GLN cc_start: 0.8373 (tm-30) cc_final: 0.7921 (tt0) REVERT: B 262 LEU cc_start: 0.9239 (mt) cc_final: 0.8893 (mp) REVERT: B 278 GLU cc_start: 0.8094 (tt0) cc_final: 0.7843 (tt0) REVERT: B 309 CYS cc_start: 0.6608 (t) cc_final: 0.6368 (t) REVERT: C 108 ASP cc_start: 0.6736 (m-30) cc_final: 0.6488 (m-30) REVERT: C 155 MET cc_start: 0.8034 (mmm) cc_final: 0.7758 (tpt) REVERT: C 217 ASN cc_start: 0.7389 (m110) cc_final: 0.6381 (t0) REVERT: C 278 GLU cc_start: 0.8189 (tt0) cc_final: 0.7925 (tt0) REVERT: C 309 CYS cc_start: 0.6735 (t) cc_final: 0.6489 (t) REVERT: C 403 ASN cc_start: 0.8515 (m-40) cc_final: 0.7910 (m110) outliers start: 34 outliers final: 14 residues processed: 299 average time/residue: 0.1981 time to fit residues: 86.1615 Evaluate side-chains 246 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 232 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 396 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 3 optimal weight: 4.9990 chunk 50 optimal weight: 30.0000 chunk 53 optimal weight: 0.0570 chunk 116 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS A 227 GLN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS B 227 GLN C 111 HIS C 227 GLN C 249 GLN ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.161550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.138394 restraints weight = 16623.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142301 restraints weight = 9325.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.144916 restraints weight = 6302.707| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9915 Z= 0.154 Angle : 0.644 10.631 13518 Z= 0.327 Chirality : 0.044 0.393 1512 Planarity : 0.004 0.029 1749 Dihedral : 5.498 32.057 1500 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.18 % Allowed : 17.47 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.93 (0.24), residues: 1266 helix: -0.00 (0.24), residues: 462 sheet: -1.27 (0.30), residues: 273 loop : -0.61 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.004 0.001 HIS B 111 PHE 0.020 0.001 PHE A 270 TYR 0.018 0.002 TYR C 457 ARG 0.009 0.001 ARG C 370 Details of bonding type rmsd link_NAG-ASN : bond 0.00971 ( 6) link_NAG-ASN : angle 4.85988 ( 18) hydrogen bonds : bond 0.03452 ( 484) hydrogen bonds : angle 5.49879 ( 1515) SS BOND : bond 0.00637 ( 21) SS BOND : angle 2.01852 ( 42) covalent geometry : bond 0.00322 ( 9888) covalent geometry : angle 0.61002 (13458) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 263 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8693 (tp) cc_final: 0.8319 (tt) REVERT: A 108 ASP cc_start: 0.6798 (m-30) cc_final: 0.6562 (m-30) REVERT: A 109 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7173 (tp) REVERT: A 249 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8214 (tt0) REVERT: A 278 GLU cc_start: 0.8272 (tt0) cc_final: 0.8045 (tt0) REVERT: A 280 ARG cc_start: 0.8674 (mtt180) cc_final: 0.8294 (mtm180) REVERT: A 309 CYS cc_start: 0.6584 (t) cc_final: 0.6290 (t) REVERT: A 425 TYR cc_start: 0.8527 (t80) cc_final: 0.7048 (t80) REVERT: A 430 LEU cc_start: 0.9092 (tp) cc_final: 0.8816 (tt) REVERT: B 109 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7243 (tp) REVERT: B 217 ASN cc_start: 0.7503 (m110) cc_final: 0.6815 (t0) REVERT: B 242 PHE cc_start: 0.8671 (m-80) cc_final: 0.8404 (m-80) REVERT: B 249 GLN cc_start: 0.8516 (tm-30) cc_final: 0.7959 (tt0) REVERT: B 262 LEU cc_start: 0.9241 (mt) cc_final: 0.8849 (mp) REVERT: B 309 CYS cc_start: 0.6574 (t) cc_final: 0.6316 (t) REVERT: B 422 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8793 (mmtm) REVERT: C 60 LEU cc_start: 0.8766 (tp) cc_final: 0.8477 (tt) REVERT: C 108 ASP cc_start: 0.6799 (m-30) cc_final: 0.6526 (m-30) REVERT: C 109 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6866 (tp) REVERT: C 242 PHE cc_start: 0.8634 (m-80) cc_final: 0.8351 (m-80) REVERT: C 280 ARG cc_start: 0.8796 (mtt180) cc_final: 0.8225 (mtt180) REVERT: C 309 CYS cc_start: 0.6641 (t) cc_final: 0.6392 (t) outliers start: 39 outliers final: 22 residues processed: 285 average time/residue: 0.1921 time to fit residues: 79.3987 Evaluate side-chains 258 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 417 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 0.8980 chunk 92 optimal weight: 0.0170 chunk 48 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 29 optimal weight: 0.0870 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 HIS C 249 GLN ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.163449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.139858 restraints weight = 16626.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.143943 restraints weight = 9384.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.146673 restraints weight = 6311.805| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9915 Z= 0.121 Angle : 0.628 10.513 13518 Z= 0.318 Chirality : 0.043 0.349 1512 Planarity : 0.004 0.026 1749 Dihedral : 5.140 27.438 1500 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.75 % Allowed : 19.94 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.36 (0.24), residues: 1266 helix: 0.70 (0.25), residues: 444 sheet: -1.18 (0.32), residues: 264 loop : -0.36 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.003 0.001 HIS A 251 PHE 0.014 0.001 PHE A 270 TYR 0.017 0.001 TYR C 68 ARG 0.005 0.001 ARG C 100 Details of bonding type rmsd link_NAG-ASN : bond 0.01110 ( 6) link_NAG-ASN : angle 4.70313 ( 18) hydrogen bonds : bond 0.03295 ( 484) hydrogen bonds : angle 5.38001 ( 1515) SS BOND : bond 0.00308 ( 21) SS BOND : angle 2.27919 ( 42) covalent geometry : bond 0.00260 ( 9888) covalent geometry : angle 0.59208 (13458) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7062 (tp) REVERT: A 278 GLU cc_start: 0.8264 (tt0) cc_final: 0.7889 (tt0) REVERT: A 326 MET cc_start: 0.7369 (mmm) cc_final: 0.6415 (mmm) REVERT: A 341 TYR cc_start: 0.7136 (m-10) cc_final: 0.6265 (m-10) REVERT: A 425 TYR cc_start: 0.8492 (t80) cc_final: 0.7187 (t80) REVERT: A 430 LEU cc_start: 0.9109 (tp) cc_final: 0.8816 (tt) REVERT: B 60 LEU cc_start: 0.8547 (tp) cc_final: 0.8292 (tt) REVERT: B 109 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6998 (tp) REVERT: B 217 ASN cc_start: 0.7306 (m110) cc_final: 0.6665 (t0) REVERT: B 249 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8052 (tt0) REVERT: B 262 LEU cc_start: 0.9234 (mt) cc_final: 0.8957 (mp) REVERT: B 309 CYS cc_start: 0.6567 (t) cc_final: 0.6313 (t) REVERT: B 314 GLU cc_start: 0.7100 (mp0) cc_final: 0.6745 (mp0) REVERT: C 60 LEU cc_start: 0.8598 (tp) cc_final: 0.8312 (tt) REVERT: C 109 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6847 (tp) REVERT: C 217 ASN cc_start: 0.7295 (m110) cc_final: 0.6559 (t0) REVERT: C 280 ARG cc_start: 0.8806 (mtt180) cc_final: 0.8222 (mtt180) REVERT: C 341 TYR cc_start: 0.7581 (m-10) cc_final: 0.6806 (m-10) outliers start: 35 outliers final: 21 residues processed: 267 average time/residue: 0.1887 time to fit residues: 72.9317 Evaluate side-chains 253 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 417 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 3 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 63 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.162029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.138450 restraints weight = 16506.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.142457 restraints weight = 9415.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145155 restraints weight = 6373.921| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9915 Z= 0.141 Angle : 0.613 9.597 13518 Z= 0.309 Chirality : 0.043 0.350 1512 Planarity : 0.004 0.027 1749 Dihedral : 4.846 26.327 1500 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.54 % Allowed : 21.22 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.17 (0.25), residues: 1266 helix: 0.97 (0.25), residues: 441 sheet: -1.01 (0.31), residues: 270 loop : -0.40 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 234 HIS 0.003 0.001 HIS B 328 PHE 0.012 0.001 PHE A 270 TYR 0.017 0.001 TYR C 68 ARG 0.004 0.001 ARG C 100 Details of bonding type rmsd link_NAG-ASN : bond 0.01022 ( 6) link_NAG-ASN : angle 4.39650 ( 18) hydrogen bonds : bond 0.03240 ( 484) hydrogen bonds : angle 5.14022 ( 1515) SS BOND : bond 0.00333 ( 21) SS BOND : angle 2.04711 ( 42) covalent geometry : bond 0.00304 ( 9888) covalent geometry : angle 0.58173 (13458) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7135 (tp) REVERT: A 278 GLU cc_start: 0.8201 (tt0) cc_final: 0.7994 (tt0) REVERT: A 326 MET cc_start: 0.7284 (mmm) cc_final: 0.6766 (mmm) REVERT: A 341 TYR cc_start: 0.7369 (m-10) cc_final: 0.6356 (m-10) REVERT: A 425 TYR cc_start: 0.8540 (t80) cc_final: 0.7242 (t80) REVERT: A 430 LEU cc_start: 0.9119 (tp) cc_final: 0.8872 (tp) REVERT: B 60 LEU cc_start: 0.8551 (tp) cc_final: 0.8346 (tt) REVERT: B 109 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7082 (tp) REVERT: B 249 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8010 (tt0) REVERT: B 262 LEU cc_start: 0.9250 (mt) cc_final: 0.8876 (mp) REVERT: B 278 GLU cc_start: 0.8093 (tt0) cc_final: 0.7866 (tt0) REVERT: B 309 CYS cc_start: 0.6589 (t) cc_final: 0.6321 (t) REVERT: B 328 HIS cc_start: 0.7919 (p90) cc_final: 0.7421 (p90) REVERT: C 109 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6919 (tp) REVERT: C 217 ASN cc_start: 0.7466 (m110) cc_final: 0.6679 (t0) outliers start: 33 outliers final: 22 residues processed: 255 average time/residue: 0.1820 time to fit residues: 67.8876 Evaluate side-chains 242 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 217 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 366 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 91 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 0.3980 chunk 58 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 HIS ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.163062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.139113 restraints weight = 16548.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.143197 restraints weight = 9419.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.145897 restraints weight = 6378.860| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9915 Z= 0.123 Angle : 0.593 9.539 13518 Z= 0.295 Chirality : 0.043 0.341 1512 Planarity : 0.003 0.025 1749 Dihedral : 4.659 24.400 1500 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.54 % Allowed : 22.94 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.09 (0.25), residues: 1266 helix: 1.46 (0.26), residues: 423 sheet: -0.92 (0.29), residues: 312 loop : -0.34 (0.29), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 47 HIS 0.003 0.001 HIS B 328 PHE 0.028 0.001 PHE B 101 TYR 0.012 0.001 TYR C 68 ARG 0.003 0.000 ARG C 100 Details of bonding type rmsd link_NAG-ASN : bond 0.01054 ( 6) link_NAG-ASN : angle 4.30045 ( 18) hydrogen bonds : bond 0.03105 ( 484) hydrogen bonds : angle 5.02233 ( 1515) SS BOND : bond 0.00349 ( 21) SS BOND : angle 1.66766 ( 42) covalent geometry : bond 0.00265 ( 9888) covalent geometry : angle 0.56529 (13458) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 232 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8405 (tp) cc_final: 0.8167 (tt) REVERT: A 109 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7047 (tp) REVERT: A 280 ARG cc_start: 0.8638 (mtt180) cc_final: 0.8121 (mtt180) REVERT: A 326 MET cc_start: 0.7283 (mmm) cc_final: 0.6590 (mmm) REVERT: A 341 TYR cc_start: 0.7301 (m-10) cc_final: 0.5950 (m-10) REVERT: A 422 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8301 (mmtm) REVERT: A 425 TYR cc_start: 0.8489 (t80) cc_final: 0.7191 (t80) REVERT: A 430 LEU cc_start: 0.9070 (tp) cc_final: 0.8859 (tp) REVERT: B 60 LEU cc_start: 0.8456 (tp) cc_final: 0.8207 (tt) REVERT: B 108 ASP cc_start: 0.6439 (m-30) cc_final: 0.5884 (m-30) REVERT: B 109 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7076 (tp) REVERT: B 249 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8021 (tt0) REVERT: B 262 LEU cc_start: 0.9251 (mt) cc_final: 0.8904 (mp) REVERT: B 278 GLU cc_start: 0.8110 (tt0) cc_final: 0.7870 (tt0) REVERT: B 309 CYS cc_start: 0.6560 (t) cc_final: 0.6258 (t) REVERT: B 314 GLU cc_start: 0.7063 (mp0) cc_final: 0.6807 (mp0) REVERT: B 328 HIS cc_start: 0.8042 (p90) cc_final: 0.7533 (p90) REVERT: C 108 ASP cc_start: 0.6591 (m-30) cc_final: 0.6060 (m-30) REVERT: C 109 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6954 (tp) REVERT: C 217 ASN cc_start: 0.7457 (m110) cc_final: 0.6676 (t0) REVERT: C 254 ASP cc_start: 0.7546 (t0) cc_final: 0.7335 (t0) REVERT: C 341 TYR cc_start: 0.7526 (m-10) cc_final: 0.7114 (m-10) outliers start: 33 outliers final: 20 residues processed: 251 average time/residue: 0.1748 time to fit residues: 64.5861 Evaluate side-chains 234 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 417 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 67 optimal weight: 0.5980 chunk 42 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS C 437 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.158947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.134554 restraints weight = 16841.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.138666 restraints weight = 9711.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141156 restraints weight = 6602.768| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9915 Z= 0.219 Angle : 0.662 9.164 13518 Z= 0.333 Chirality : 0.045 0.328 1512 Planarity : 0.004 0.034 1749 Dihedral : 4.779 24.695 1500 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.11 % Allowed : 22.94 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.11 (0.25), residues: 1266 helix: 1.46 (0.26), residues: 423 sheet: -0.90 (0.30), residues: 285 loop : -0.36 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 234 HIS 0.006 0.002 HIS C 111 PHE 0.025 0.002 PHE B 101 TYR 0.018 0.002 TYR C 68 ARG 0.002 0.000 ARG A 280 Details of bonding type rmsd link_NAG-ASN : bond 0.00865 ( 6) link_NAG-ASN : angle 4.13141 ( 18) hydrogen bonds : bond 0.03390 ( 484) hydrogen bonds : angle 5.05408 ( 1515) SS BOND : bond 0.00571 ( 21) SS BOND : angle 2.35108 ( 42) covalent geometry : bond 0.00477 ( 9888) covalent geometry : angle 0.63268 (13458) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 227 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8500 (tp) cc_final: 0.8268 (tt) REVERT: A 109 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7452 (tp) REVERT: A 278 GLU cc_start: 0.8258 (tt0) cc_final: 0.8013 (tt0) REVERT: B 60 LEU cc_start: 0.8559 (tp) cc_final: 0.8344 (tt) REVERT: B 68 TYR cc_start: 0.9101 (t80) cc_final: 0.8886 (t80) REVERT: B 108 ASP cc_start: 0.6609 (m-30) cc_final: 0.6052 (m-30) REVERT: B 249 GLN cc_start: 0.8605 (tm-30) cc_final: 0.7560 (tm-30) REVERT: B 309 CYS cc_start: 0.6644 (t) cc_final: 0.6334 (t) REVERT: B 314 GLU cc_start: 0.7235 (mp0) cc_final: 0.6989 (mp0) REVERT: B 437 GLN cc_start: 0.8831 (mt0) cc_final: 0.8550 (mt0) REVERT: C 109 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7171 (tp) REVERT: C 224 ASP cc_start: 0.8854 (t0) cc_final: 0.8504 (t0) outliers start: 29 outliers final: 20 residues processed: 244 average time/residue: 0.1892 time to fit residues: 67.5722 Evaluate side-chains 230 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 366 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 122 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 14 optimal weight: 0.0270 chunk 94 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 71 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.162573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.138355 restraints weight = 16755.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.142507 restraints weight = 9549.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.145228 restraints weight = 6460.609| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9915 Z= 0.123 Angle : 0.614 9.190 13518 Z= 0.304 Chirality : 0.043 0.327 1512 Planarity : 0.004 0.026 1749 Dihedral : 4.527 22.462 1500 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.11 % Allowed : 24.44 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.26 (0.25), residues: 1266 helix: 1.48 (0.26), residues: 426 sheet: -0.75 (0.31), residues: 285 loop : -0.22 (0.29), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 234 HIS 0.003 0.001 HIS B 328 PHE 0.023 0.001 PHE B 101 TYR 0.011 0.001 TYR A 399 ARG 0.003 0.000 ARG A 207 Details of bonding type rmsd link_NAG-ASN : bond 0.01058 ( 6) link_NAG-ASN : angle 4.07658 ( 18) hydrogen bonds : bond 0.03107 ( 484) hydrogen bonds : angle 4.95534 ( 1515) SS BOND : bond 0.00311 ( 21) SS BOND : angle 1.64236 ( 42) covalent geometry : bond 0.00264 ( 9888) covalent geometry : angle 0.58966 (13458) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 109 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7123 (tp) REVERT: A 341 TYR cc_start: 0.7346 (m-10) cc_final: 0.6951 (m-10) REVERT: A 425 TYR cc_start: 0.8471 (t80) cc_final: 0.6955 (t80) REVERT: B 60 LEU cc_start: 0.8531 (tp) cc_final: 0.8275 (tt) REVERT: B 249 GLN cc_start: 0.8642 (tm-30) cc_final: 0.7419 (tm-30) REVERT: B 280 ARG cc_start: 0.8760 (mtt180) cc_final: 0.8029 (mtt180) REVERT: B 309 CYS cc_start: 0.6526 (t) cc_final: 0.6219 (t) REVERT: B 314 GLU cc_start: 0.7262 (mp0) cc_final: 0.7050 (mp0) REVERT: C 109 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6980 (tp) REVERT: C 278 GLU cc_start: 0.8316 (tt0) cc_final: 0.8064 (tt0) outliers start: 29 outliers final: 22 residues processed: 238 average time/residue: 0.1939 time to fit residues: 67.9151 Evaluate side-chains 238 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 366 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 58 optimal weight: 6.9990 chunk 106 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.160959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.136680 restraints weight = 16620.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.140777 restraints weight = 9593.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.143246 restraints weight = 6520.664| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9915 Z= 0.174 Angle : 0.648 9.047 13518 Z= 0.323 Chirality : 0.043 0.324 1512 Planarity : 0.004 0.029 1749 Dihedral : 4.566 22.842 1500 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.43 % Allowed : 23.69 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.29 (0.25), residues: 1266 helix: 1.43 (0.26), residues: 426 sheet: -0.75 (0.31), residues: 285 loop : -0.14 (0.29), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 234 HIS 0.004 0.001 HIS B 328 PHE 0.019 0.001 PHE B 101 TYR 0.015 0.002 TYR A 230 ARG 0.002 0.000 ARG A 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00935 ( 6) link_NAG-ASN : angle 4.02009 ( 18) hydrogen bonds : bond 0.03266 ( 484) hydrogen bonds : angle 4.94506 ( 1515) SS BOND : bond 0.00445 ( 21) SS BOND : angle 1.99315 ( 42) covalent geometry : bond 0.00379 ( 9888) covalent geometry : angle 0.62265 (13458) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8965 (t80) cc_final: 0.8618 (t80) REVERT: A 109 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7293 (tp) REVERT: A 280 ARG cc_start: 0.8875 (mtt180) cc_final: 0.8555 (mtt180) REVERT: A 326 MET cc_start: 0.7160 (mmm) cc_final: 0.6335 (mmm) REVERT: A 341 TYR cc_start: 0.7339 (m-10) cc_final: 0.5949 (m-10) REVERT: A 425 TYR cc_start: 0.8527 (t80) cc_final: 0.7034 (t80) REVERT: B 60 LEU cc_start: 0.8449 (tp) cc_final: 0.8240 (tt) REVERT: B 108 ASP cc_start: 0.6478 (m-30) cc_final: 0.5924 (m-30) REVERT: B 217 ASN cc_start: 0.7379 (m-40) cc_final: 0.6591 (t0) REVERT: B 249 GLN cc_start: 0.8620 (tm-30) cc_final: 0.7498 (tm-30) REVERT: B 309 CYS cc_start: 0.6594 (t) cc_final: 0.6277 (t) REVERT: B 314 GLU cc_start: 0.7309 (mp0) cc_final: 0.7050 (mp0) REVERT: C 109 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7087 (tp) REVERT: C 224 ASP cc_start: 0.8836 (t0) cc_final: 0.8499 (t0) REVERT: C 278 GLU cc_start: 0.8337 (tt0) cc_final: 0.8093 (tt0) outliers start: 32 outliers final: 26 residues processed: 234 average time/residue: 0.1749 time to fit residues: 60.2315 Evaluate side-chains 240 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 366 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 4 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 121 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.161143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.136761 restraints weight = 16834.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.140834 restraints weight = 9620.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.143576 restraints weight = 6514.022| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9915 Z= 0.156 Angle : 0.661 10.832 13518 Z= 0.328 Chirality : 0.043 0.321 1512 Planarity : 0.004 0.039 1749 Dihedral : 4.505 21.779 1500 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.22 % Allowed : 23.69 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.34 (0.25), residues: 1266 helix: 1.44 (0.26), residues: 426 sheet: -0.69 (0.31), residues: 285 loop : -0.10 (0.29), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 234 HIS 0.003 0.001 HIS A 251 PHE 0.019 0.001 PHE B 101 TYR 0.015 0.001 TYR A 230 ARG 0.003 0.000 ARG B 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00991 ( 6) link_NAG-ASN : angle 3.97545 ( 18) hydrogen bonds : bond 0.03236 ( 484) hydrogen bonds : angle 4.94046 ( 1515) SS BOND : bond 0.00372 ( 21) SS BOND : angle 1.83439 ( 42) covalent geometry : bond 0.00342 ( 9888) covalent geometry : angle 0.63806 (13458) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 109 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7260 (tp) REVERT: A 278 GLU cc_start: 0.8256 (tt0) cc_final: 0.8010 (tt0) REVERT: A 280 ARG cc_start: 0.8852 (mtt180) cc_final: 0.8409 (mtt180) REVERT: A 326 MET cc_start: 0.7047 (mmm) cc_final: 0.6239 (mmm) REVERT: A 341 TYR cc_start: 0.7260 (m-10) cc_final: 0.5718 (m-10) REVERT: A 425 TYR cc_start: 0.8490 (t80) cc_final: 0.7081 (t80) REVERT: B 60 LEU cc_start: 0.8464 (tp) cc_final: 0.8213 (tt) REVERT: B 217 ASN cc_start: 0.7399 (m-40) cc_final: 0.6594 (t0) REVERT: B 249 GLN cc_start: 0.8625 (tm-30) cc_final: 0.7497 (tm-30) REVERT: B 309 CYS cc_start: 0.6586 (t) cc_final: 0.6306 (t) REVERT: B 314 GLU cc_start: 0.7315 (mp0) cc_final: 0.7053 (mp0) REVERT: C 109 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7021 (tp) REVERT: C 224 ASP cc_start: 0.8792 (t0) cc_final: 0.8464 (t0) REVERT: C 278 GLU cc_start: 0.8334 (tt0) cc_final: 0.8089 (tt0) REVERT: C 437 GLN cc_start: 0.8732 (mt0) cc_final: 0.8520 (mt0) outliers start: 30 outliers final: 24 residues processed: 230 average time/residue: 0.1702 time to fit residues: 57.6811 Evaluate side-chains 240 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 366 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 95 optimal weight: 0.5980 chunk 80 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 45 optimal weight: 0.0040 chunk 101 optimal weight: 0.1980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.163061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140072 restraints weight = 16688.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.144057 restraints weight = 9380.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.146748 restraints weight = 6302.654| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9915 Z= 0.115 Angle : 0.643 12.206 13518 Z= 0.315 Chirality : 0.043 0.322 1512 Planarity : 0.004 0.040 1749 Dihedral : 4.304 20.581 1500 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.36 % Allowed : 24.01 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.52 (0.25), residues: 1266 helix: 1.58 (0.26), residues: 426 sheet: -0.53 (0.32), residues: 285 loop : -0.01 (0.30), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 234 HIS 0.005 0.001 HIS A 328 PHE 0.018 0.001 PHE B 101 TYR 0.010 0.001 TYR B 457 ARG 0.004 0.001 ARG B 65 Details of bonding type rmsd link_NAG-ASN : bond 0.01097 ( 6) link_NAG-ASN : angle 3.95916 ( 18) hydrogen bonds : bond 0.03015 ( 484) hydrogen bonds : angle 4.85846 ( 1515) SS BOND : bond 0.00336 ( 21) SS BOND : angle 1.53168 ( 42) covalent geometry : bond 0.00253 ( 9888) covalent geometry : angle 0.62173 (13458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3225.86 seconds wall clock time: 57 minutes 2.80 seconds (3422.80 seconds total)