Starting phenix.real_space_refine on Fri Sep 11 09:48:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pum_71872/09_2026/9pum_71872.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pum_71872/09_2026/9pum_71872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pum_71872/09_2026/9pum_71872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pum_71872/09_2026/9pum_71872.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pum_71872/09_2026/9pum_71872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pum_71872/09_2026/9pum_71872.map" } resolution = 2.8 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= 0.023 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 50 5.16 5 C 5390 2.51 5 N 1466 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8572 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 898 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "I" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 898 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "A" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3346 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 400} Chain breaks: 1 Chain: "B" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3346 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 400} Chain breaks: 1 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.82, per 1000 atoms: 0.21 Number of scatterers: 8572 At special positions: 0 Unit cell: (93.06, 117.5, 83.66, 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 50 16.00 O 1666 8.00 N 1466 7.00 C 5390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 571 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 256 " - pdb=" SG CYS A 269 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 469 " distance=2.03 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 544 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 571 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 256 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 469 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 473 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 544 " 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 308 " " NAG A 602 " - " ASN A 351 " " NAG A 603 " - " ASN A 523 " " NAG B 601 " - " ASN B 308 " " NAG B 602 " - " ASN B 351 " " NAG B 603 " - " ASN B 523 " Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 399.2 milliseconds 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 23 sheets defined 6.9% alpha, 43.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 368 No H-bonds generated for 'chain 'A' and resid 367 through 368' Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 368 No H-bonds generated for 'chain 'B' and resid 367 through 368' Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 400 through 404 Processing sheet with id=AA1, first strand: chain 'H' and resid 2 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.503A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER H 97 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE H 31 " --> pdb=" O SER H 97 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ASN H 32 " --> pdb=" O THR H 52 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR H 52 " --> pdb=" O ASN H 32 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N MET H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.503A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU H 100B" --> pdb=" O PRO H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 2 through 7 Processing sheet with id=AA5, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.504A pdb=" N GLY I 33 " --> pdb=" O VAL I 95 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER I 97 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE I 31 " --> pdb=" O SER I 97 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ASN I 32 " --> pdb=" O THR I 52 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N THR I 52 " --> pdb=" O ASN I 32 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N MET I 34 " --> pdb=" O LEU I 50 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 11 through 12 removed outlier: 7.119A pdb=" N LEU I 100B" --> pdb=" O PRO I 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.336A pdb=" N ALA A 528 " --> pdb=" O ASN A 551 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ASN A 551 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR A 530 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 164 through 166 Processing sheet with id=AA9, first strand: chain 'A' and resid 178 through 184 removed outlier: 4.484A pdb=" N LEU A 181 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU B 181 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 190 through 198 removed outlier: 6.533A pdb=" N THR A 206 " --> pdb=" O PRO A 194 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU A 196 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA A 204 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 228 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR A 230 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU A 239 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 254 through 260 removed outlier: 4.428A pdb=" N CYS A 256 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU A 268 " --> pdb=" O CYS A 256 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 258 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TYR A 266 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 310 through 311 removed outlier: 4.676A pdb=" N ILE A 332 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 315 through 320 removed outlier: 3.512A pdb=" N ALA A 317 " --> pdb=" O GLY A 339 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG A 376 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 410 through 413 removed outlier: 4.526A pdb=" N GLN A 433 " --> pdb=" O THR A 423 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU A 434 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N THR A 440 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASP A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 481 through 483 Processing sheet with id=AB7, first strand: chain 'B' and resid 148 through 150 removed outlier: 6.342A pdb=" N ALA B 528 " --> pdb=" O ASN B 551 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ASN B 551 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR B 530 " --> pdb=" O GLU B 549 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AB9, first strand: chain 'B' and resid 190 through 198 removed outlier: 6.533A pdb=" N THR B 206 " --> pdb=" O PRO B 194 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU B 196 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA B 204 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 228 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR B 230 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU B 239 " --> pdb=" O THR B 230 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 254 through 260 removed outlier: 4.404A pdb=" N CYS B 256 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU B 268 " --> pdb=" O CYS B 256 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU B 258 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR B 266 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 310 through 311 removed outlier: 6.834A pdb=" N SER B 310 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE B 332 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 315 through 320 removed outlier: 3.550A pdb=" N ALA B 317 " --> pdb=" O GLY B 339 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG B 376 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 410 through 413 removed outlier: 4.498A pdb=" N GLN B 433 " --> pdb=" O THR B 423 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU B 434 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N THR B 440 " --> pdb=" O ASP B 444 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ASP B 444 " --> pdb=" O THR B 440 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 481 through 483 309 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2762 1.34 - 1.46: 1729 1.46 - 1.58: 4207 1.58 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 8766 Sorted by residual: bond pdb=" N THR A 143 " pdb=" CA THR A 143 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N THR B 143 " pdb=" CA THR B 143 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" N GLN I 1 " pdb=" CA GLN I 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" CG1 ILE A 567 " pdb=" CD1 ILE A 567 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.69e+00 ... (remaining 8761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 10875 1.04 - 2.08: 812 2.08 - 3.12: 158 3.12 - 4.16: 69 4.16 - 5.20: 22 Bond angle restraints: 11936 Sorted by residual: angle pdb=" N THR A 426 " pdb=" CA THR A 426 " pdb=" C THR A 426 " ideal model delta sigma weight residual 109.83 104.63 5.20 1.55e+00 4.16e-01 1.13e+01 angle pdb=" N THR B 426 " pdb=" CA THR B 426 " pdb=" C THR B 426 " ideal model delta sigma weight residual 109.83 104.68 5.15 1.55e+00 4.16e-01 1.11e+01 angle pdb=" N PRO A 324 " pdb=" CA PRO A 324 " pdb=" C PRO A 324 " ideal model delta sigma weight residual 111.34 116.35 -5.01 1.55e+00 4.16e-01 1.05e+01 angle pdb=" N PRO B 324 " pdb=" CA PRO B 324 " pdb=" C PRO B 324 " ideal model delta sigma weight residual 111.34 116.17 -4.83 1.55e+00 4.16e-01 9.73e+00 angle pdb=" N LYS A 431 " pdb=" CA LYS A 431 " pdb=" C LYS A 431 " ideal model delta sigma weight residual 108.79 104.27 4.52 1.53e+00 4.27e-01 8.72e+00 ... (remaining 11931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.51: 4789 14.51 - 29.01: 383 29.01 - 43.52: 133 43.52 - 58.03: 31 58.03 - 72.53: 8 Dihedral angle restraints: 5344 sinusoidal: 2188 harmonic: 3156 Sorted by residual: dihedral pdb=" CA THR B 426 " pdb=" C THR B 426 " pdb=" N SER B 427 " pdb=" CA SER B 427 " ideal model delta harmonic sigma weight residual 180.00 -150.23 -29.77 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA THR A 426 " pdb=" C THR A 426 " pdb=" N SER A 427 " pdb=" CA SER A 427 " ideal model delta harmonic sigma weight residual -180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ILE A 421 " pdb=" C ILE A 421 " pdb=" N TYR A 422 " pdb=" CA TYR A 422 " ideal model delta harmonic sigma weight residual 180.00 156.64 23.36 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 5341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1154 0.066 - 0.133: 195 0.133 - 0.199: 13 0.199 - 0.265: 0 0.265 - 0.332: 2 Chirality restraints: 1364 Sorted by residual: chirality pdb=" C1 NAG A 603 " pdb=" ND2 ASN A 523 " pdb=" C2 NAG A 603 " pdb=" O5 NAG A 603 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C1 NAG B 603 " pdb=" ND2 ASN B 523 " pdb=" C2 NAG B 603 " pdb=" O5 NAG B 603 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA ILE B 228 " pdb=" N ILE B 228 " pdb=" C ILE B 228 " pdb=" CB ILE B 228 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 1361 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 38 " 0.187 9.50e-02 1.11e+02 8.46e-02 5.71e+00 pdb=" NE ARG I 38 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG I 38 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG I 38 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG I 38 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 38 " 0.186 9.50e-02 1.11e+02 8.39e-02 5.61e+00 pdb=" NE ARG H 38 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG H 38 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG H 38 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG H 38 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 66 " 0.163 9.50e-02 1.11e+02 7.38e-02 4.41e+00 pdb=" NE ARG H 66 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG H 66 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG H 66 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG H 66 " -0.000 2.00e-02 2.50e+03 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 3715 2.93 - 3.42: 7935 3.42 - 3.91: 14290 3.91 - 4.41: 16796 4.41 - 4.90: 28065 Nonbonded interactions: 70801 Sorted by model distance: nonbonded pdb=" OD1 ASN A 208 " pdb=" OE1 GLN A 222 " model vdw 2.433 3.040 nonbonded pdb=" OD1 ASN B 208 " pdb=" OE1 GLN B 222 " model vdw 2.436 3.040 nonbonded pdb=" N ASP B 264 " pdb=" OD1 ASP B 264 " model vdw 2.487 3.120 nonbonded pdb=" N ASP A 264 " pdb=" OD1 ASP A 264 " model vdw 2.490 3.120 nonbonded pdb=" O TRP I 100 " pdb=" NH2 ARG B 192 " model vdw 2.517 3.120 ... (remaining 70796 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: 0.01 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'A' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.780 Find NCS groups from input model: 0.040 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:5.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 : 0.005 0.051 8788 Z= 0.205 Angle : 0.694 5.201 11986 Z= 0.368 Chirality : 0.050 0.332 1364 Planarity : 0.007 0.085 1520 Dihedral : 12.557 72.532 3284 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.62 % Allowed : 16.32 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.24), residues: 1084 helix: -1.02 (0.87), residues: 32 sheet: -0.77 (0.24), residues: 474 loop : -1.43 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.003 ARG I 38 TYR 0.028 0.003 TYR B 205 PHE 0.023 0.002 PHE B 156 TRP 0.013 0.003 TRP A 406 HIS 0.005 0.002 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 ( 8766) covalent geometry : angle 0.68740 / 0.37 (11936) SS BOND : bond 0.00272 / 0.17 ( 16) SS BOND : angle 1.04485 / 0.73 ( 32) hydrogen bonds : bond 0.21442 / 14.13 ( 300) hydrogen bonds : angle 9.84340 / 6.88 ( 762) link_NAG-ASN : bond 0.00421 / 0.20 ( 6) link_NAG-ASN : angle 2.36691 / 1.59 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 191 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 90 TYR cc_start: 0.7928 (m-80) cc_final: 0.7488 (m-80) REVERT: I 34 MET cc_start: 0.8516 (mtp) cc_final: 0.8177 (mtp) REVERT: A 291 ASP cc_start: 0.7071 (m-30) cc_final: 0.6613 (m-30) REVERT: A 358 LYS cc_start: 0.8587 (mptt) cc_final: 0.8201 (mmtp) REVERT: A 484 LEU cc_start: 0.6187 (mt) cc_final: 0.5955 (mt) REVERT: A 549 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7697 (mt-10) REVERT: B 291 ASP cc_start: 0.7035 (m-30) cc_final: 0.6395 (m-30) REVERT: B 536 ILE cc_start: 0.5605 (pt) cc_final: 0.5333 (pt) REVERT: B 549 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7881 (mt-10) outliers start: 6 outliers final: 4 residues processed: 197 average time/residue: 0.3680 time to fit residues: 79.4728 Evaluate side-chains 168 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 164 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 264 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.0980 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN A 461 ASN B 461 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.149627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.138815 restraints weight = 11427.848| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.78 r_work: 0.3788 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8788 Z= 0.134 Angle : 0.601 6.962 11986 Z= 0.313 Chirality : 0.047 0.209 1364 Planarity : 0.005 0.052 1520 Dihedral : 5.654 69.734 1326 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.47 % Allowed : 14.76 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.24), residues: 1084 helix: -0.65 (0.82), residues: 34 sheet: -0.29 (0.24), residues: 464 loop : -1.22 (0.23), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 173 TYR 0.028 0.002 TYR B 327 PHE 0.021 0.002 PHE B 156 TRP 0.014 0.001 TRP B 406 HIS 0.003 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 8766) covalent geometry : angle 0.59616 / 0.31 (11936) SS BOND : bond 0.00215 / 0.13 ( 16) SS BOND : angle 0.65640 / 0.42 ( 32) hydrogen bonds : bond 0.04169 / 2.95 ( 300) hydrogen bonds : angle 6.78075 / 4.67 ( 762) link_NAG-ASN : bond 0.00442 / 0.20 ( 6) link_NAG-ASN : angle 2.01875 / 1.29 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 173 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 34 MET cc_start: 0.8615 (mtp) cc_final: 0.8399 (mtp) REVERT: A 248 ASN cc_start: 0.7752 (t0) cc_final: 0.7476 (t0) REVERT: A 533 THR cc_start: 0.7300 (m) cc_final: 0.7053 (t) REVERT: A 536 ILE cc_start: 0.5637 (pt) cc_final: 0.5164 (pt) REVERT: B 224 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7208 (tt) REVERT: B 376 ARG cc_start: 0.7782 (mmt90) cc_final: 0.7562 (mpt-90) REVERT: B 386 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8170 (tttm) REVERT: B 536 ILE cc_start: 0.5615 (pt) cc_final: 0.5377 (pt) outliers start: 43 outliers final: 18 residues processed: 196 average time/residue: 0.3480 time to fit residues: 74.8130 Evaluate side-chains 191 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 561 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 83 optimal weight: 0.0870 chunk 94 optimal weight: 0.0670 chunk 31 optimal weight: 0.0040 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.2908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN B 248 ASN B 250 ASN B 461 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.150733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.139930 restraints weight = 11292.389| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.79 r_work: 0.3799 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8788 Z= 0.115 Angle : 0.565 8.153 11986 Z= 0.289 Chirality : 0.045 0.207 1364 Planarity : 0.005 0.053 1520 Dihedral : 5.295 67.818 1320 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.43 % Allowed : 16.53 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.24), residues: 1084 helix: -0.27 (0.83), residues: 34 sheet: -0.00 (0.25), residues: 456 loop : -1.22 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 242 TYR 0.020 0.001 TYR B 327 PHE 0.018 0.002 PHE B 156 TRP 0.016 0.001 TRP B 406 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 8766) covalent geometry : angle 0.56270 / 0.29 (11936) SS BOND : bond 0.00195 / 0.11 ( 16) SS BOND : angle 0.56582 / 0.37 ( 32) hydrogen bonds : bond 0.03661 / 2.61 ( 300) hydrogen bonds : angle 6.04107 / 4.15 ( 762) link_NAG-ASN : bond 0.00453 / 0.20 ( 6) link_NAG-ASN : angle 1.39518 / 0.93 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 82 SER cc_start: 0.8595 (t) cc_final: 0.8276 (p) REVERT: I 34 MET cc_start: 0.8567 (mtp) cc_final: 0.8351 (mtp) REVERT: I 82 SER cc_start: 0.8864 (t) cc_final: 0.8527 (p) REVERT: A 248 ASN cc_start: 0.7757 (t0) cc_final: 0.7469 (t0) REVERT: A 468 SER cc_start: 0.8347 (m) cc_final: 0.8000 (t) REVERT: A 536 ILE cc_start: 0.5635 (pt) cc_final: 0.5239 (pt) REVERT: B 219 LYS cc_start: 0.8333 (mttp) cc_final: 0.8113 (mtpp) REVERT: B 224 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7169 (tt) REVERT: B 376 ARG cc_start: 0.7826 (mmt90) cc_final: 0.7593 (mpt-90) REVERT: B 386 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8198 (tttm) REVERT: B 425 SER cc_start: 0.7994 (m) cc_final: 0.7616 (t) outliers start: 33 outliers final: 18 residues processed: 196 average time/residue: 0.3506 time to fit residues: 75.5169 Evaluate side-chains 190 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 561 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 0.0770 chunk 63 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN B 248 ASN B 461 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.146807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.135880 restraints weight = 11579.383| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.82 r_work: 0.3770 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8788 Z= 0.174 Angle : 0.597 8.603 11986 Z= 0.304 Chirality : 0.047 0.251 1364 Planarity : 0.005 0.054 1520 Dihedral : 5.391 66.850 1318 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.09 % Allowed : 17.36 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.24), residues: 1084 helix: -0.45 (0.81), residues: 34 sheet: 0.12 (0.25), residues: 428 loop : -1.32 (0.22), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 242 TYR 0.035 0.002 TYR A 327 PHE 0.020 0.002 PHE B 156 TRP 0.017 0.002 TRP A 406 HIS 0.004 0.001 HIS B 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 8766) covalent geometry : angle 0.59242 / 0.30 (11936) SS BOND : bond 0.00285 / 0.15 ( 16) SS BOND : angle 0.76911 / 0.49 ( 32) hydrogen bonds : bond 0.03792 / 2.67 ( 300) hydrogen bonds : angle 5.95559 / 4.08 ( 762) link_NAG-ASN : bond 0.00528 / 0.23 ( 6) link_NAG-ASN : angle 1.96469 / 1.29 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 34 MET cc_start: 0.8617 (mtp) cc_final: 0.8396 (mtp) REVERT: I 82 SER cc_start: 0.8865 (t) cc_final: 0.8513 (p) REVERT: A 248 ASN cc_start: 0.7765 (t0) cc_final: 0.7467 (t0) REVERT: A 536 ILE cc_start: 0.5698 (pt) cc_final: 0.5305 (pt) REVERT: A 564 LYS cc_start: 0.7806 (mtmt) cc_final: 0.7586 (mtpm) REVERT: B 224 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7216 (tt) REVERT: B 248 ASN cc_start: 0.7737 (t0) cc_final: 0.7442 (t0) REVERT: B 386 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8282 (tttm) REVERT: B 425 SER cc_start: 0.7956 (m) cc_final: 0.7614 (t) outliers start: 49 outliers final: 25 residues processed: 201 average time/residue: 0.3409 time to fit residues: 75.3284 Evaluate side-chains 194 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 532 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 57 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN B 461 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.148396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.137990 restraints weight = 11348.184| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.77 r_work: 0.3773 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8788 Z= 0.198 Angle : 0.619 8.158 11986 Z= 0.314 Chirality : 0.048 0.263 1364 Planarity : 0.005 0.056 1520 Dihedral : 5.532 66.157 1318 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.89 % Allowed : 17.57 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.24), residues: 1084 helix: -0.52 (0.80), residues: 34 sheet: 0.13 (0.26), residues: 414 loop : -1.46 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 242 TYR 0.035 0.002 TYR A 327 PHE 0.020 0.002 PHE B 156 TRP 0.017 0.002 TRP B 406 HIS 0.005 0.001 HIS B 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 ( 8766) covalent geometry : angle 0.61406 / 0.31 (11936) SS BOND : bond 0.00316 / 0.17 ( 16) SS BOND : angle 0.85795 / 0.55 ( 32) hydrogen bonds : bond 0.03870 / 2.72 ( 300) hydrogen bonds : angle 5.93739 / 4.07 ( 762) link_NAG-ASN : bond 0.00549 / 0.21 ( 6) link_NAG-ASN : angle 1.98654 / 1.28 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 170 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 90 TYR cc_start: 0.7917 (m-80) cc_final: 0.7423 (m-80) REVERT: I 34 MET cc_start: 0.8646 (mtp) cc_final: 0.8431 (mtp) REVERT: I 82 SER cc_start: 0.8847 (t) cc_final: 0.8493 (p) REVERT: I 90 TYR cc_start: 0.7884 (m-80) cc_final: 0.7375 (m-80) REVERT: A 248 ASN cc_start: 0.7743 (t0) cc_final: 0.7435 (t0) REVERT: A 536 ILE cc_start: 0.5690 (pt) cc_final: 0.5307 (pt) REVERT: B 175 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7285 (mtp) REVERT: B 224 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7222 (tp) outliers start: 47 outliers final: 32 residues processed: 194 average time/residue: 0.3163 time to fit residues: 67.7377 Evaluate side-chains 204 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 532 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN I 32 ASN B 248 ASN B 250 ASN B 461 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.145035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.134679 restraints weight = 11247.912| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.75 r_work: 0.3754 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 8788 Z= 0.295 Angle : 0.698 9.077 11986 Z= 0.357 Chirality : 0.051 0.300 1364 Planarity : 0.006 0.061 1520 Dihedral : 6.014 64.421 1318 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 5.72 % Allowed : 18.50 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.24), residues: 1084 helix: -0.87 (0.79), residues: 34 sheet: -0.01 (0.26), residues: 426 loop : -1.57 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 376 TYR 0.037 0.002 TYR A 327 PHE 0.026 0.003 PHE B 156 TRP 0.019 0.002 TRP A 406 HIS 0.008 0.002 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.30 ( 8766) covalent geometry : angle 0.69168 / 0.36 (11936) SS BOND : bond 0.00456 / 0.24 ( 16) SS BOND : angle 1.14495 / 0.72 ( 32) hydrogen bonds : bond 0.04384 / 3.06 ( 300) hydrogen bonds : angle 6.15527 / 4.22 ( 762) link_NAG-ASN : bond 0.00388 / 0.17 ( 6) link_NAG-ASN : angle 2.23035 / 1.45 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 178 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 90 TYR cc_start: 0.7931 (m-80) cc_final: 0.7455 (m-80) REVERT: I 82 SER cc_start: 0.8810 (t) cc_final: 0.8446 (p) REVERT: I 90 TYR cc_start: 0.7924 (m-80) cc_final: 0.7535 (m-80) REVERT: A 219 LYS cc_start: 0.8429 (mtpp) cc_final: 0.8225 (mttp) REVERT: A 248 ASN cc_start: 0.7780 (t0) cc_final: 0.7453 (t0) REVERT: A 536 ILE cc_start: 0.5713 (pt) cc_final: 0.5319 (pt) REVERT: A 564 LYS cc_start: 0.7860 (mtmt) cc_final: 0.7628 (mtpm) REVERT: B 175 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7306 (mtp) REVERT: B 219 LYS cc_start: 0.8430 (mttp) cc_final: 0.8218 (mtpp) REVERT: B 224 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7276 (tp) REVERT: B 248 ASN cc_start: 0.7814 (t0) cc_final: 0.7509 (t0) outliers start: 55 outliers final: 34 residues processed: 204 average time/residue: 0.3423 time to fit residues: 77.0948 Evaluate side-chains 208 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain B residue 561 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN I 32 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.148491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.137939 restraints weight = 11313.511| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.79 r_work: 0.3769 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8788 Z= 0.196 Angle : 0.650 8.925 11986 Z= 0.328 Chirality : 0.048 0.310 1364 Planarity : 0.005 0.050 1520 Dihedral : 5.785 61.591 1318 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.68 % Allowed : 20.37 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.24), residues: 1084 helix: -0.71 (0.80), residues: 34 sheet: 0.06 (0.26), residues: 428 loop : -1.58 (0.22), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 173 TYR 0.041 0.002 TYR A 327 PHE 0.017 0.002 PHE A 156 TRP 0.018 0.002 TRP A 406 HIS 0.005 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 ( 8766) covalent geometry : angle 0.64377 / 0.33 (11936) SS BOND : bond 0.00345 / 0.19 ( 16) SS BOND : angle 0.97294 / 0.67 ( 32) hydrogen bonds : bond 0.03830 / 2.70 ( 300) hydrogen bonds : angle 5.93812 / 4.07 ( 762) link_NAG-ASN : bond 0.00417 / 0.18 ( 6) link_NAG-ASN : angle 2.15634 / 1.40 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 90 TYR cc_start: 0.7880 (m-80) cc_final: 0.7408 (m-80) REVERT: I 82 SER cc_start: 0.8796 (t) cc_final: 0.8438 (p) REVERT: I 90 TYR cc_start: 0.7908 (m-80) cc_final: 0.7542 (m-80) REVERT: A 248 ASN cc_start: 0.7729 (t0) cc_final: 0.7416 (t0) REVERT: A 536 ILE cc_start: 0.5665 (pt) cc_final: 0.5449 (pt) REVERT: A 549 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.5406 (mp0) REVERT: A 564 LYS cc_start: 0.7869 (mtmt) cc_final: 0.7635 (mtpm) REVERT: B 175 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7263 (mtp) REVERT: B 219 LYS cc_start: 0.8433 (mttp) cc_final: 0.8166 (mtpt) REVERT: B 224 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7252 (tp) REVERT: B 248 ASN cc_start: 0.7783 (t0) cc_final: 0.7512 (t0) REVERT: B 468 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.7849 (t) outliers start: 45 outliers final: 30 residues processed: 194 average time/residue: 0.3617 time to fit residues: 76.6540 Evaluate side-chains 207 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 532 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 78 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 2 optimal weight: 0.0170 chunk 102 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN I 32 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN B 461 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.149759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.139136 restraints weight = 11291.994| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 1.80 r_work: 0.3786 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8788 Z= 0.140 Angle : 0.603 8.530 11986 Z= 0.303 Chirality : 0.047 0.280 1364 Planarity : 0.005 0.049 1520 Dihedral : 5.436 57.375 1318 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.64 % Allowed : 21.52 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.24), residues: 1084 helix: -0.39 (0.84), residues: 34 sheet: 0.12 (0.25), residues: 428 loop : -1.53 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 173 TYR 0.032 0.001 TYR A 327 PHE 0.016 0.002 PHE B 156 TRP 0.015 0.001 TRP B 406 HIS 0.004 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 8766) covalent geometry : angle 0.59839 / 0.30 (11936) SS BOND : bond 0.00255 / 0.14 ( 16) SS BOND : angle 0.81605 / 0.61 ( 32) hydrogen bonds : bond 0.03461 / 2.44 ( 300) hydrogen bonds : angle 5.72512 / 3.93 ( 762) link_NAG-ASN : bond 0.00477 / 0.21 ( 6) link_NAG-ASN : angle 1.91008 / 1.27 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 90 TYR cc_start: 0.7873 (m-80) cc_final: 0.7386 (m-80) REVERT: A 242 ARG cc_start: 0.8063 (ttt180) cc_final: 0.7772 (ttp80) REVERT: A 248 ASN cc_start: 0.7754 (t0) cc_final: 0.7437 (t0) REVERT: A 475 THR cc_start: 0.8265 (t) cc_final: 0.8054 (p) REVERT: A 536 ILE cc_start: 0.5580 (pt) cc_final: 0.5183 (pt) REVERT: A 549 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.5332 (mp0) REVERT: B 175 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7242 (mtp) REVERT: B 224 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7193 (tt) REVERT: B 248 ASN cc_start: 0.7757 (t0) cc_final: 0.7499 (t0) REVERT: B 468 SER cc_start: 0.8385 (m) cc_final: 0.7920 (t) outliers start: 35 outliers final: 24 residues processed: 190 average time/residue: 0.3520 time to fit residues: 73.4005 Evaluate side-chains 199 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 532 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 71 optimal weight: 0.0570 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN I 32 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN B 267 GLN B 461 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.149632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.139060 restraints weight = 11306.670| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 1.79 r_work: 0.3791 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8788 Z= 0.138 Angle : 0.596 8.444 11986 Z= 0.300 Chirality : 0.047 0.291 1364 Planarity : 0.005 0.049 1520 Dihedral : 5.239 51.861 1318 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.43 % Allowed : 22.04 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.24), residues: 1084 helix: -0.23 (0.86), residues: 34 sheet: 0.17 (0.25), residues: 428 loop : -1.49 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 173 TYR 0.036 0.001 TYR B 327 PHE 0.015 0.002 PHE B 156 TRP 0.014 0.001 TRP B 406 HIS 0.004 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 8766) covalent geometry : angle 0.59101 / 0.30 (11936) SS BOND : bond 0.00255 / 0.14 ( 16) SS BOND : angle 0.75292 / 0.53 ( 32) hydrogen bonds : bond 0.03400 / 2.40 ( 300) hydrogen bonds : angle 5.60934 / 3.85 ( 762) link_NAG-ASN : bond 0.00482 / 0.22 ( 6) link_NAG-ASN : angle 1.90385 / 1.26 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 90 TYR cc_start: 0.7884 (m-80) cc_final: 0.7524 (m-80) REVERT: A 242 ARG cc_start: 0.8065 (ttt180) cc_final: 0.7771 (ttp80) REVERT: A 248 ASN cc_start: 0.7740 (t0) cc_final: 0.7425 (t0) REVERT: A 536 ILE cc_start: 0.5588 (pt) cc_final: 0.5192 (pt) REVERT: A 549 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.5325 (mp0) REVERT: B 175 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7229 (mtp) REVERT: B 224 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7270 (tt) REVERT: B 248 ASN cc_start: 0.7723 (t0) cc_final: 0.7499 (t0) REVERT: B 468 SER cc_start: 0.8476 (m) cc_final: 0.8005 (t) REVERT: B 475 THR cc_start: 0.8058 (t) cc_final: 0.7823 (p) outliers start: 33 outliers final: 25 residues processed: 189 average time/residue: 0.3720 time to fit residues: 77.1067 Evaluate side-chains 200 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 532 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 30 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN I 32 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.149639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.138975 restraints weight = 11313.145| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.80 r_work: 0.3783 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8788 Z= 0.176 Angle : 0.629 10.052 11986 Z= 0.316 Chirality : 0.048 0.293 1364 Planarity : 0.005 0.049 1520 Dihedral : 5.287 48.876 1318 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.43 % Allowed : 22.45 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.25), residues: 1084 helix: -0.28 (0.86), residues: 34 sheet: 0.19 (0.26), residues: 428 loop : -1.51 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 173 TYR 0.044 0.002 TYR B 327 PHE 0.017 0.002 PHE B 156 TRP 0.015 0.002 TRP B 406 HIS 0.004 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 ( 8766) covalent geometry : angle 0.62568 / 0.31 (11936) SS BOND : bond 0.00289 / 0.15 ( 16) SS BOND : angle 0.82402 / 0.57 ( 32) hydrogen bonds : bond 0.03543 / 2.48 ( 300) hydrogen bonds : angle 5.64601 / 3.87 ( 762) link_NAG-ASN : bond 0.00663 / 0.25 ( 6) link_NAG-ASN : angle 1.55633 / 0.97 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 90 TYR cc_start: 0.7917 (m-80) cc_final: 0.7419 (m-80) REVERT: A 175 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7462 (mtm) REVERT: A 242 ARG cc_start: 0.8053 (ttt180) cc_final: 0.7763 (ttp80) REVERT: A 248 ASN cc_start: 0.7758 (t0) cc_final: 0.7450 (t0) REVERT: A 536 ILE cc_start: 0.5608 (pt) cc_final: 0.5209 (pp) REVERT: B 175 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7286 (mtp) REVERT: B 219 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7865 (mtpp) REVERT: B 224 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7268 (tt) REVERT: B 248 ASN cc_start: 0.7743 (t0) cc_final: 0.7524 (t0) REVERT: B 468 SER cc_start: 0.8495 (m) cc_final: 0.8018 (t) outliers start: 33 outliers final: 22 residues processed: 188 average time/residue: 0.3705 time to fit residues: 76.5696 Evaluate side-chains 194 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 532 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN I 32 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** 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 = 0.4006 r_free = 0.4006 target = 0.149372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.138675 restraints weight = 11319.943| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.81 r_work: 0.3780 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8788 Z= 0.180 Angle : 0.638 13.951 11986 Z= 0.320 Chirality : 0.048 0.289 1364 Planarity : 0.005 0.051 1520 Dihedral : 5.259 40.689 1318 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.53 % Allowed : 22.45 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.25), residues: 1084 helix: -0.35 (0.85), residues: 34 sheet: 0.17 (0.26), residues: 428 loop : -1.52 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 173 TYR 0.046 0.002 TYR B 327 PHE 0.018 0.002 PHE B 156 TRP 0.019 0.002 TRP B 406 HIS 0.004 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 8766) covalent geometry : angle 0.63437 / 0.32 (11936) SS BOND : bond 0.00287 / 0.16 ( 16) SS BOND : angle 0.84464 / 0.57 ( 32) hydrogen bonds : bond 0.03633 / 2.54 ( 300) hydrogen bonds : angle 5.73658 / 3.93 ( 762) link_NAG-ASN : bond 0.00615 / 0.24 ( 6) link_NAG-ASN : angle 1.64618 / 1.06 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2766.13 seconds wall clock time: 47 minutes 58.13 seconds (2878.13 seconds total)