Starting phenix.real_space_refine on Thu Sep 18 02:18:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ibh_52810/09_2025/9ibh_52810.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ibh_52810/09_2025/9ibh_52810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ibh_52810/09_2025/9ibh_52810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ibh_52810/09_2025/9ibh_52810.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ibh_52810/09_2025/9ibh_52810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ibh_52810/09_2025/9ibh_52810.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 64 5.16 5 C 8043 2.51 5 N 2269 2.21 5 O 2530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12906 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4146 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 24, 'TRANS': 520} Chain: "B" Number of atoms: 4146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4146 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 24, 'TRANS': 520} Chain: "C" Number of atoms: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4150 Classifications: {'peptide': 546} Link IDs: {'PTRANS': 24, 'TRANS': 521} Chain: "D" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 417 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 8, 'TRANS': 46} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 3.34, per 1000 atoms: 0.26 Number of scatterers: 12906 At special positions: 0 Unit cell: (91.98, 108.77, 112.42, 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 64 16.00 O 2530 8.00 N 2269 7.00 C 8043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 745.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 13 sheets defined 39.6% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 85 through 100 Proline residue: A 98 - end of helix Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 125 through 142 removed outlier: 4.291A pdb=" N VAL A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 197 through 212 removed outlier: 3.590A pdb=" N ALA A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 205 " --> pdb=" O MET A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'A' and resid 239 through 258 removed outlier: 5.280A pdb=" N SER A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ARG A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 285 Processing helix chain 'A' and resid 289 through 311 removed outlier: 3.535A pdb=" N LEU A 293 " --> pdb=" O ASP A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 398 through 413 removed outlier: 3.888A pdb=" N GLY A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 454 removed outlier: 3.647A pdb=" N ALA A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 515 through 539 Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 85 through 100 Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 125 through 141 removed outlier: 4.236A pdb=" N VAL B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'B' and resid 239 through 258 removed outlier: 5.745A pdb=" N SER B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ARG B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 283 Processing helix chain 'B' and resid 289 through 312 Processing helix chain 'B' and resid 358 through 362 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.640A pdb=" N VAL B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 413 removed outlier: 4.552A pdb=" N ALA B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 453 removed outlier: 3.587A pdb=" N ALA B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 489 removed outlier: 3.667A pdb=" N ASP B 486 " --> pdb=" O GLY B 483 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N HIS B 487 " --> pdb=" O ASP B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 541 removed outlier: 3.676A pdb=" N ALA B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 85 through 100 Proline residue: C 98 - end of helix Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 125 through 141 removed outlier: 4.277A pdb=" N VAL C 129 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 172 removed outlier: 3.768A pdb=" N GLU C 172 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 212 through 227 Processing helix chain 'C' and resid 239 through 259 removed outlier: 6.100A pdb=" N SER C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ARG C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 285 Processing helix chain 'C' and resid 289 through 311 removed outlier: 3.645A pdb=" N LEU C 293 " --> pdb=" O ASP C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 362 Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 397 through 413 removed outlier: 4.250A pdb=" N ALA C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 453 removed outlier: 3.607A pdb=" N ALA C 441 " --> pdb=" O SER C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 489 removed outlier: 3.868A pdb=" N ASP C 486 " --> pdb=" O GLY C 483 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N HIS C 487 " --> pdb=" O ASP C 484 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY C 489 " --> pdb=" O ASP C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 541 removed outlier: 3.804A pdb=" N ALA C 540 " --> pdb=" O VAL C 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 1049 through 1053 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11 removed outlier: 6.099A pdb=" N ALA A 39 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 163 removed outlier: 4.161A pdb=" N TYR A 156 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU A 175 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 10.565A pdb=" N GLU A 190 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N ASP A 508 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N GLU A 192 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N GLN A 506 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N GLU A 194 " --> pdb=" O ALA A 504 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N ALA A 504 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 327 through 331 removed outlier: 6.014A pdb=" N GLN A 349 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 377 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N SER A 429 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N HIS A 379 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE A 431 " --> pdb=" O HIS A 379 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ASN A 381 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N GLU A 433 " --> pdb=" O ASN A 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 366 Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 11 removed outlier: 6.252A pdb=" N ALA B 39 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR B 60 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALA B 115 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASN B 62 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL B 117 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLN B 64 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N SER B 119 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 161 through 163 removed outlier: 3.590A pdb=" N GLY B 181 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR B 156 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU B 175 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP B 176 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER B 191 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL B 178 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL B 189 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA B 180 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 10.428A pdb=" N GLU B 190 " --> pdb=" O ASP B 508 " (cutoff:3.500A) removed outlier: 10.359A pdb=" N ASP B 508 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 10.061A pdb=" N GLU B 192 " --> pdb=" O GLN B 506 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N GLN B 506 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N GLU B 194 " --> pdb=" O ALA B 504 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N ALA B 504 " --> pdb=" O GLU B 194 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER B 498 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN B 474 " --> pdb=" O GLU B 471 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 323 through 324 Processing sheet with id=AA8, first strand: chain 'B' and resid 376 through 381 removed outlier: 6.348A pdb=" N LEU B 377 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N SER B 429 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS B 379 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE B 431 " --> pdb=" O HIS B 379 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASN B 381 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLU B 433 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLN B 349 " --> pdb=" O THR B 432 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 363 through 367 removed outlier: 3.591A pdb=" N GLU B 367 " --> pdb=" O GLY B 370 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 5 through 11 removed outlier: 6.082A pdb=" N ALA C 39 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR C 60 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ALA C 115 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASN C 62 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL C 117 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLN C 64 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N SER C 119 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 160 through 163 removed outlier: 3.999A pdb=" N TYR C 156 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU C 175 " --> pdb=" O TYR C 156 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP C 176 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER C 191 " --> pdb=" O ASP C 176 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL C 178 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL C 189 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA C 180 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N GLU C 190 " --> pdb=" O ASP C 508 " (cutoff:3.500A) removed outlier: 10.249A pdb=" N ASP C 508 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 10.087A pdb=" N GLU C 192 " --> pdb=" O GLN C 506 " (cutoff:3.500A) removed outlier: 9.881A pdb=" N GLN C 506 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N GLU C 194 " --> pdb=" O ALA C 504 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N ALA C 504 " --> pdb=" O GLU C 194 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 376 through 381 removed outlier: 6.381A pdb=" N LEU C 377 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N SER C 429 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N HIS C 379 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE C 431 " --> pdb=" O HIS C 379 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASN C 381 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLU C 433 " --> pdb=" O ASN C 381 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN C 349 " --> pdb=" O THR C 432 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 363 through 367 732 hydrogen bonds defined for protein. 1974 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: 2.43 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3114 1.33 - 1.45: 2326 1.45 - 1.57: 7498 1.57 - 1.69: 0 1.69 - 1.81: 125 Bond restraints: 13063 Sorted by residual: bond pdb=" CA SER B 503 " pdb=" CB SER B 503 " ideal model delta sigma weight residual 1.536 1.470 0.066 1.42e-02 4.96e+03 2.16e+01 bond pdb=" CA SER B 498 " pdb=" CB SER B 498 " ideal model delta sigma weight residual 1.530 1.455 0.075 1.61e-02 3.86e+03 2.14e+01 bond pdb=" CA SER B 479 " pdb=" CB SER B 479 " ideal model delta sigma weight residual 1.529 1.462 0.068 1.64e-02 3.72e+03 1.70e+01 bond pdb=" CA SER B 197 " pdb=" CB SER B 197 " ideal model delta sigma weight residual 1.527 1.469 0.058 1.44e-02 4.82e+03 1.61e+01 bond pdb=" CA SER B 85 " pdb=" CB SER B 85 " ideal model delta sigma weight residual 1.528 1.472 0.056 1.54e-02 4.22e+03 1.32e+01 ... (remaining 13058 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 17171 2.73 - 5.45: 489 5.45 - 8.18: 34 8.18 - 10.90: 4 10.90 - 13.63: 2 Bond angle restraints: 17700 Sorted by residual: angle pdb=" CA GLN C 520 " pdb=" CB GLN C 520 " pdb=" CG GLN C 520 " ideal model delta sigma weight residual 114.10 127.30 -13.20 2.00e+00 2.50e-01 4.35e+01 angle pdb=" C ARG D1063 " pdb=" CA ARG D1063 " pdb=" CB ARG D1063 " ideal model delta sigma weight residual 110.08 102.85 7.23 1.15e+00 7.56e-01 3.95e+01 angle pdb=" CG ARG C 253 " pdb=" CD ARG C 253 " pdb=" NE ARG C 253 " ideal model delta sigma weight residual 112.00 125.63 -13.63 2.20e+00 2.07e-01 3.84e+01 angle pdb=" N ASP B 285 " pdb=" CA ASP B 285 " pdb=" C ASP B 285 " ideal model delta sigma weight residual 113.15 107.16 5.99 1.19e+00 7.06e-01 2.54e+01 angle pdb=" CA ARG C 253 " pdb=" CB ARG C 253 " pdb=" CG ARG C 253 " ideal model delta sigma weight residual 114.10 104.10 10.00 2.00e+00 2.50e-01 2.50e+01 ... (remaining 17695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 7120 17.67 - 35.33: 624 35.33 - 53.00: 176 53.00 - 70.66: 47 70.66 - 88.33: 19 Dihedral angle restraints: 7986 sinusoidal: 3169 harmonic: 4817 Sorted by residual: dihedral pdb=" CD ARG B 266 " pdb=" NE ARG B 266 " pdb=" CZ ARG B 266 " pdb=" NH1 ARG B 266 " ideal model delta sinusoidal sigma weight residual 0.00 88.33 -88.33 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CD ARG B 360 " pdb=" NE ARG B 360 " pdb=" CZ ARG B 360 " pdb=" NH1 ARG B 360 " ideal model delta sinusoidal sigma weight residual 0.00 86.92 -86.92 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CD ARG C 398 " pdb=" NE ARG C 398 " pdb=" CZ ARG C 398 " pdb=" NH1 ARG C 398 " ideal model delta sinusoidal sigma weight residual 0.00 86.67 -86.67 1 1.00e+01 1.00e-02 9.04e+01 ... (remaining 7983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1808 0.097 - 0.194: 207 0.194 - 0.290: 19 0.290 - 0.387: 1 0.387 - 0.484: 1 Chirality restraints: 2036 Sorted by residual: chirality pdb=" CB ILE C 260 " pdb=" CA ILE C 260 " pdb=" CG1 ILE C 260 " pdb=" CG2 ILE C 260 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" CA VAL B 186 " pdb=" N VAL B 186 " pdb=" C VAL B 186 " pdb=" CB VAL B 186 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ARG D1063 " pdb=" N ARG D1063 " pdb=" C ARG D1063 " pdb=" CB ARG D1063 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 2033 not shown) Planarity restraints: 2349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 398 " 1.110 9.50e-02 1.11e+02 4.97e-01 1.49e+02 pdb=" NE ARG C 398 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG C 398 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG C 398 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG C 398 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 360 " 1.106 9.50e-02 1.11e+02 4.96e-01 1.48e+02 pdb=" NE ARG B 360 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG B 360 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 360 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 360 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 315 " -1.078 9.50e-02 1.11e+02 4.83e-01 1.41e+02 pdb=" NE ARG B 315 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 315 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 315 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 315 " -0.020 2.00e-02 2.50e+03 ... (remaining 2346 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 220 2.67 - 3.22: 11613 3.22 - 3.78: 19813 3.78 - 4.34: 28879 4.34 - 4.90: 46850 Nonbonded interactions: 107375 Sorted by model distance: nonbonded pdb=" OH TYR B 380 " pdb=" OG SER B 438 " model vdw 2.108 3.040 nonbonded pdb=" NH2 ARG C 253 " pdb=" OE1 GLU C 276 " model vdw 2.267 3.120 nonbonded pdb=" OH TYR C 258 " pdb=" OE2 GLU C 301 " model vdw 2.287 3.040 nonbonded pdb=" O TYR B 161 " pdb=" O HOH B 601 " model vdw 2.311 3.040 nonbonded pdb=" NE ARG A 66 " pdb=" OE2 GLU B 430 " model vdw 2.322 3.120 ... (remaining 107370 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 1 through 545) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.450 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.570 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 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 : 0.006 0.078 13063 Z= 0.380 Angle : 0.984 13.625 17700 Z= 0.624 Chirality : 0.061 0.484 2036 Planarity : 0.038 0.497 2349 Dihedral : 15.649 88.331 4890 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.85 % Allowed : 3.00 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.20), residues: 1683 helix: -1.32 (0.19), residues: 571 sheet: 1.33 (0.24), residues: 417 loop : -0.99 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.069 0.008 ARG C 259 TYR 0.039 0.003 TYR A 423 PHE 0.065 0.003 PHE B 493 TRP 0.011 0.001 TRP B 233 HIS 0.027 0.002 HIS C 403 Details of bonding type rmsd covalent geometry : bond 0.00619 (13063) covalent geometry : angle 0.98441 (17700) hydrogen bonds : bond 0.13823 ( 732) hydrogen bonds : angle 6.12932 ( 1974) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.593 Fit side-chains REVERT: A 86 GLU cc_start: 0.8044 (tt0) cc_final: 0.7781 (pt0) REVERT: A 110 GLU cc_start: 0.8359 (tt0) cc_final: 0.8158 (tt0) REVERT: B 86 GLU cc_start: 0.7804 (tt0) cc_final: 0.7453 (mm-30) REVERT: B 258 TYR cc_start: 0.8376 (m-80) cc_final: 0.7944 (m-80) REVERT: B 280 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: B 523 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8868 (mp) outliers start: 39 outliers final: 9 residues processed: 193 average time/residue: 0.8289 time to fit residues: 170.8762 Evaluate side-chains 123 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 397 LYS Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 GLN B 212 GLN C 212 GLN C 403 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.101284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.069118 restraints weight = 18348.612| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.53 r_work: 0.2693 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13063 Z= 0.203 Angle : 0.590 5.564 17700 Z= 0.316 Chirality : 0.045 0.178 2036 Planarity : 0.006 0.065 2349 Dihedral : 5.446 59.424 1850 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.24 % Allowed : 9.44 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.20), residues: 1683 helix: 1.16 (0.21), residues: 567 sheet: 1.69 (0.25), residues: 401 loop : -0.48 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 266 TYR 0.021 0.002 TYR C 380 PHE 0.026 0.002 PHE C 493 TRP 0.006 0.001 TRP B 233 HIS 0.009 0.001 HIS C 403 Details of bonding type rmsd covalent geometry : bond 0.00455 (13063) covalent geometry : angle 0.58967 (17700) hydrogen bonds : bond 0.05116 ( 732) hydrogen bonds : angle 4.47148 ( 1974) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.508 Fit side-chains REVERT: B 86 GLU cc_start: 0.8095 (tt0) cc_final: 0.7609 (mm-30) REVERT: B 405 ARG cc_start: 0.8232 (tpt90) cc_final: 0.7948 (tpp80) REVERT: C 398 ARG cc_start: 0.6945 (mtp-110) cc_final: 0.6555 (mtt180) outliers start: 17 outliers final: 2 residues processed: 134 average time/residue: 0.8232 time to fit residues: 118.1589 Evaluate side-chains 112 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 508 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 117 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 93 optimal weight: 0.0570 chunk 31 optimal weight: 6.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.103127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.071404 restraints weight = 18433.431| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.50 r_work: 0.2738 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13063 Z= 0.110 Angle : 0.492 5.455 17700 Z= 0.260 Chirality : 0.043 0.160 2036 Planarity : 0.004 0.065 2349 Dihedral : 4.072 25.935 1829 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.88 % Allowed : 11.63 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.21), residues: 1683 helix: 2.49 (0.22), residues: 567 sheet: 1.78 (0.25), residues: 401 loop : -0.23 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 259 TYR 0.016 0.001 TYR A 267 PHE 0.017 0.001 PHE C 493 TRP 0.004 0.001 TRP B 233 HIS 0.002 0.000 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00240 (13063) covalent geometry : angle 0.49185 (17700) hydrogen bonds : bond 0.03915 ( 732) hydrogen bonds : angle 4.06193 ( 1974) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.585 Fit side-chains REVERT: A 399 ARG cc_start: 0.6795 (mtm-85) cc_final: 0.6246 (mpp80) REVERT: B 405 ARG cc_start: 0.8207 (tpt90) cc_final: 0.7960 (tpp80) REVERT: C 280 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6925 (tm-30) REVERT: C 398 ARG cc_start: 0.7021 (mtp-110) cc_final: 0.6739 (mtt90) REVERT: C 423 TYR cc_start: 0.8282 (m-10) cc_final: 0.8035 (m-10) REVERT: C 466 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8001 (mtm) REVERT: D 1017 MET cc_start: 0.7507 (tmm) cc_final: 0.7247 (tmm) outliers start: 12 outliers final: 3 residues processed: 125 average time/residue: 0.8553 time to fit residues: 114.2283 Evaluate side-chains 114 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 492 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 38 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 51 optimal weight: 0.0980 chunk 133 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 520 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.100510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.069223 restraints weight = 18611.532| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.46 r_work: 0.2696 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13063 Z= 0.154 Angle : 0.505 5.974 17700 Z= 0.268 Chirality : 0.043 0.160 2036 Planarity : 0.004 0.065 2349 Dihedral : 4.114 20.200 1827 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.10 % Allowed : 12.36 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.21), residues: 1683 helix: 2.78 (0.22), residues: 567 sheet: 1.93 (0.25), residues: 401 loop : -0.12 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 360 TYR 0.020 0.002 TYR C 380 PHE 0.018 0.001 PHE C 493 TRP 0.003 0.001 TRP C 231 HIS 0.003 0.001 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00352 (13063) covalent geometry : angle 0.50540 (17700) hydrogen bonds : bond 0.04351 ( 732) hydrogen bonds : angle 4.09866 ( 1974) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.571 Fit side-chains REVERT: B 405 ARG cc_start: 0.8214 (tpt90) cc_final: 0.7958 (tpp80) REVERT: C 280 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6964 (tt0) REVERT: C 398 ARG cc_start: 0.6939 (mtp-110) cc_final: 0.6666 (mtt90) REVERT: C 466 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.7965 (mtm) REVERT: C 520 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7837 (tp40) REVERT: D 1018 THR cc_start: 0.8259 (m) cc_final: 0.7925 (p) outliers start: 15 outliers final: 5 residues processed: 130 average time/residue: 0.8021 time to fit residues: 111.9836 Evaluate side-chains 123 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 520 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 148 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 113 optimal weight: 0.0670 chunk 60 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 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 = 0.3374 r_free = 0.3374 target = 0.101947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.069968 restraints weight = 18585.508| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.52 r_work: 0.2680 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13063 Z= 0.121 Angle : 0.481 6.503 17700 Z= 0.255 Chirality : 0.043 0.161 2036 Planarity : 0.004 0.065 2349 Dihedral : 3.991 20.456 1827 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.95 % Allowed : 13.24 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.21), residues: 1683 helix: 2.96 (0.22), residues: 567 sheet: 1.93 (0.25), residues: 401 loop : -0.03 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 360 TYR 0.015 0.002 TYR A 267 PHE 0.015 0.001 PHE C 493 TRP 0.003 0.000 TRP B 233 HIS 0.002 0.001 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00269 (13063) covalent geometry : angle 0.48089 (17700) hydrogen bonds : bond 0.03898 ( 732) hydrogen bonds : angle 3.97758 ( 1974) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.544 Fit side-chains REVERT: A 7 ARG cc_start: 0.8129 (mmt-90) cc_final: 0.7899 (mmt-90) REVERT: B 259 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.7808 (mtt90) REVERT: B 405 ARG cc_start: 0.8176 (tpt90) cc_final: 0.7927 (tpp80) REVERT: C 280 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6952 (tt0) REVERT: C 398 ARG cc_start: 0.7011 (mtp-110) cc_final: 0.6757 (mtt90) REVERT: C 466 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.7984 (mtm) REVERT: D 1017 MET cc_start: 0.7579 (tmm) cc_final: 0.7307 (tmm) REVERT: D 1018 THR cc_start: 0.8150 (m) cc_final: 0.7891 (p) REVERT: D 1019 ARG cc_start: 0.8450 (ptp-110) cc_final: 0.8137 (ttm-80) outliers start: 13 outliers final: 8 residues processed: 128 average time/residue: 0.8409 time to fit residues: 115.3243 Evaluate side-chains 125 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain D residue 1014 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 87 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.099692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.068420 restraints weight = 18580.982| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.45 r_work: 0.2681 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13063 Z= 0.171 Angle : 0.511 6.404 17700 Z= 0.271 Chirality : 0.044 0.163 2036 Planarity : 0.004 0.065 2349 Dihedral : 4.165 21.223 1827 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.54 % Allowed : 12.66 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.21), residues: 1683 helix: 2.91 (0.22), residues: 567 sheet: 1.94 (0.25), residues: 401 loop : -0.01 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D1063 TYR 0.021 0.002 TYR C 380 PHE 0.018 0.001 PHE C 493 TRP 0.002 0.001 TRP B 233 HIS 0.003 0.001 HIS C 403 Details of bonding type rmsd covalent geometry : bond 0.00398 (13063) covalent geometry : angle 0.51128 (17700) hydrogen bonds : bond 0.04418 ( 732) hydrogen bonds : angle 4.08149 ( 1974) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.556 Fit side-chains REVERT: A 398 ARG cc_start: 0.6345 (mtt180) cc_final: 0.6128 (mtt180) REVERT: B 259 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.7846 (mtt90) REVERT: B 405 ARG cc_start: 0.8227 (tpt90) cc_final: 0.7971 (tpp80) REVERT: C 280 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6972 (tt0) REVERT: C 398 ARG cc_start: 0.7052 (mtp-110) cc_final: 0.6840 (mtt90) REVERT: D 1017 MET cc_start: 0.7634 (tmm) cc_final: 0.7346 (tmm) REVERT: D 1018 THR cc_start: 0.8162 (m) cc_final: 0.7861 (p) REVERT: D 1019 ARG cc_start: 0.8439 (ptp-110) cc_final: 0.8129 (ttm-80) outliers start: 21 outliers final: 10 residues processed: 129 average time/residue: 0.8173 time to fit residues: 113.0466 Evaluate side-chains 125 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain D residue 1014 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 162 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.099089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.067104 restraints weight = 18464.466| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.49 r_work: 0.2623 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13063 Z= 0.226 Angle : 0.549 7.688 17700 Z= 0.291 Chirality : 0.045 0.160 2036 Planarity : 0.005 0.066 2349 Dihedral : 4.334 21.707 1827 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.61 % Allowed : 12.73 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.21), residues: 1683 helix: 2.77 (0.21), residues: 567 sheet: 1.88 (0.25), residues: 401 loop : -0.03 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1063 TYR 0.023 0.002 TYR C 380 PHE 0.019 0.002 PHE C 493 TRP 0.003 0.001 TRP A 231 HIS 0.004 0.001 HIS C 403 Details of bonding type rmsd covalent geometry : bond 0.00534 (13063) covalent geometry : angle 0.54940 (17700) hydrogen bonds : bond 0.04851 ( 732) hydrogen bonds : angle 4.17281 ( 1974) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.545 Fit side-chains REVERT: A 93 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7610 (tpt-90) REVERT: B 259 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.7886 (mtt90) REVERT: B 405 ARG cc_start: 0.8238 (tpt90) cc_final: 0.8012 (tpp-160) REVERT: C 280 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6908 (tt0) REVERT: C 298 HIS cc_start: 0.7907 (t-170) cc_final: 0.7705 (t-90) REVERT: C 398 ARG cc_start: 0.7100 (mtp-110) cc_final: 0.6885 (mtt90) REVERT: D 1017 MET cc_start: 0.7651 (tmm) cc_final: 0.7364 (tmm) REVERT: D 1018 THR cc_start: 0.8159 (m) cc_final: 0.7863 (p) REVERT: D 1019 ARG cc_start: 0.8403 (ptp-110) cc_final: 0.8079 (ttm-80) outliers start: 22 outliers final: 12 residues processed: 132 average time/residue: 0.8383 time to fit residues: 118.3196 Evaluate side-chains 130 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain D residue 1014 SER Chi-restraints excluded: chain D residue 1062 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 4 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.100699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.068663 restraints weight = 18388.126| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.49 r_work: 0.2686 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13063 Z= 0.145 Angle : 0.508 7.954 17700 Z= 0.269 Chirality : 0.044 0.180 2036 Planarity : 0.004 0.066 2349 Dihedral : 4.150 21.290 1827 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.54 % Allowed : 12.73 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.21), residues: 1683 helix: 2.91 (0.22), residues: 567 sheet: 1.86 (0.25), residues: 401 loop : 0.02 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 360 TYR 0.016 0.002 TYR C 380 PHE 0.015 0.001 PHE C 493 TRP 0.002 0.001 TRP B 233 HIS 0.003 0.001 HIS C 403 Details of bonding type rmsd covalent geometry : bond 0.00331 (13063) covalent geometry : angle 0.50804 (17700) hydrogen bonds : bond 0.04148 ( 732) hydrogen bonds : angle 4.03279 ( 1974) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.541 Fit side-chains REVERT: A 93 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7596 (tpt-90) REVERT: B 259 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.7884 (mtt90) REVERT: B 405 ARG cc_start: 0.8241 (tpt90) cc_final: 0.7965 (tpp80) REVERT: C 280 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6924 (tt0) REVERT: C 298 HIS cc_start: 0.7924 (t-170) cc_final: 0.7715 (t-90) REVERT: C 466 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.7922 (mtm) REVERT: C 520 GLN cc_start: 0.8100 (tp40) cc_final: 0.7848 (tp40) REVERT: D 1017 MET cc_start: 0.7620 (tmm) cc_final: 0.7361 (tmm) REVERT: D 1018 THR cc_start: 0.8126 (m) cc_final: 0.7885 (p) REVERT: D 1019 ARG cc_start: 0.8443 (ptp-110) cc_final: 0.8156 (ttm-80) outliers start: 21 outliers final: 10 residues processed: 130 average time/residue: 0.8283 time to fit residues: 115.1253 Evaluate side-chains 125 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain D residue 1014 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 11 optimal weight: 0.9980 chunk 139 optimal weight: 0.0000 chunk 158 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 118 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 209 HIS A 303 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.071045 restraints weight = 18540.118| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.46 r_work: 0.2733 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13063 Z= 0.103 Angle : 0.484 8.221 17700 Z= 0.254 Chirality : 0.042 0.173 2036 Planarity : 0.004 0.065 2349 Dihedral : 3.906 20.445 1827 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.24 % Allowed : 13.24 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.21), residues: 1683 helix: 3.10 (0.22), residues: 569 sheet: 1.85 (0.25), residues: 402 loop : 0.07 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D1063 TYR 0.014 0.001 TYR A 267 PHE 0.013 0.001 PHE B 493 TRP 0.003 0.000 TRP B 233 HIS 0.002 0.000 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00227 (13063) covalent geometry : angle 0.48406 (17700) hydrogen bonds : bond 0.03484 ( 732) hydrogen bonds : angle 3.85413 ( 1974) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.549 Fit side-chains REVERT: A 93 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7543 (tpt-90) REVERT: A 360 ARG cc_start: 0.8195 (tmm160) cc_final: 0.7857 (ttp80) REVERT: A 399 ARG cc_start: 0.6850 (mtm-85) cc_final: 0.6231 (mpp80) REVERT: B 259 ARG cc_start: 0.8305 (ttm-80) cc_final: 0.7902 (mtt90) REVERT: C 466 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.7939 (mtm) REVERT: C 520 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7717 (tp40) REVERT: D 1017 MET cc_start: 0.7655 (tmm) cc_final: 0.7358 (tmm) REVERT: D 1019 ARG cc_start: 0.8462 (ptp-110) cc_final: 0.8218 (ttm-80) outliers start: 17 outliers final: 6 residues processed: 123 average time/residue: 0.8233 time to fit residues: 108.7139 Evaluate side-chains 118 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 520 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 32 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 41 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.100444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.068343 restraints weight = 18412.631| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.49 r_work: 0.2649 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13063 Z= 0.178 Angle : 0.527 9.837 17700 Z= 0.278 Chirality : 0.044 0.181 2036 Planarity : 0.005 0.065 2349 Dihedral : 4.127 20.965 1827 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.88 % Allowed : 13.83 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.21), residues: 1683 helix: 2.98 (0.22), residues: 567 sheet: 1.93 (0.25), residues: 401 loop : 0.09 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D1063 TYR 0.019 0.002 TYR C 380 PHE 0.016 0.001 PHE B 493 TRP 0.002 0.001 TRP B 231 HIS 0.003 0.001 HIS C 403 Details of bonding type rmsd covalent geometry : bond 0.00417 (13063) covalent geometry : angle 0.52701 (17700) hydrogen bonds : bond 0.04279 ( 732) hydrogen bonds : angle 4.01401 ( 1974) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.572 Fit side-chains REVERT: B 259 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.7860 (mtt90) REVERT: B 260 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.7090 (mp) REVERT: B 405 ARG cc_start: 0.8226 (tpt90) cc_final: 0.7950 (tpp80) REVERT: C 298 HIS cc_start: 0.7921 (t-170) cc_final: 0.7720 (t-90) REVERT: C 466 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.7913 (mtm) REVERT: D 1017 MET cc_start: 0.7589 (tmm) cc_final: 0.7304 (tmm) REVERT: D 1019 ARG cc_start: 0.8409 (ptp-110) cc_final: 0.8138 (ttm-80) outliers start: 12 outliers final: 5 residues processed: 121 average time/residue: 0.8719 time to fit residues: 112.7962 Evaluate side-chains 120 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 492 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 10 optimal weight: 0.4980 chunk 134 optimal weight: 10.0000 chunk 136 optimal weight: 0.4980 chunk 45 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN C 209 HIS C 212 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.101855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.070809 restraints weight = 18445.155| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.45 r_work: 0.2695 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13063 Z= 0.108 Angle : 0.488 9.725 17700 Z= 0.256 Chirality : 0.043 0.177 2036 Planarity : 0.004 0.066 2349 Dihedral : 3.910 20.473 1827 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.66 % Allowed : 13.90 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.21), residues: 1683 helix: 3.16 (0.22), residues: 567 sheet: 1.89 (0.25), residues: 401 loop : 0.14 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 399 TYR 0.015 0.001 TYR A 267 PHE 0.014 0.001 PHE B 493 TRP 0.003 0.000 TRP B 233 HIS 0.002 0.000 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00240 (13063) covalent geometry : angle 0.48776 (17700) hydrogen bonds : bond 0.03554 ( 732) hydrogen bonds : angle 3.85437 ( 1974) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5220.14 seconds wall clock time: 89 minutes 41.89 seconds (5381.89 seconds total)