Starting phenix.real_space_refine on Sat Aug 23 10:21:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iux_35729/08_2025/8iux_35729.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iux_35729/08_2025/8iux_35729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iux_35729/08_2025/8iux_35729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iux_35729/08_2025/8iux_35729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iux_35729/08_2025/8iux_35729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iux_35729/08_2025/8iux_35729.map" } resolution = 3.1 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= 0.070 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 63 5.16 5 C 7104 2.51 5 N 2037 2.21 5 O 2268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11472 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3782 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 469} 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 Restraints were copied for chains: B, C Time building chain proxies: 2.79, per 1000 atoms: 0.24 Number of scatterers: 11472 At special positions: 0 Unit cell: (85.004, 85.004, 149.564, 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 63 16.00 O 2268 8.00 N 2037 7.00 C 7104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 269 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 273 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 463 " distance=2.03 Simple disulfide: pdb=" SG CYS C 5 " - pdb=" SG CYS C 463 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 67 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 67 " distance=2.03 Simple disulfide: pdb=" SG CYS B 88 " - pdb=" SG CYS B 130 " distance=2.03 Simple disulfide: pdb=" SG CYS C 88 " - pdb=" SG CYS C 130 " distance=2.03 Simple disulfide: pdb=" SG CYS B 273 " - pdb=" SG CYS B 297 " distance=2.02 Simple disulfide: pdb=" SG CYS C 273 " - pdb=" SG CYS C 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 470 " - pdb=" SG CYS C 474 " 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 501 " - " ASN A 408 " " NAG A 502 " - " ASN A 29 " " NAG A 503 " - " ASN A 480 " " NAG B 501 " - " ASN B 408 " " NAG B 502 " - " ASN B 29 " " NAG B 503 " - " ASN B 480 " " NAG C 501 " - " ASN C 408 " " NAG C 502 " - " ASN C 29 " " NAG C 503 " - " ASN C 480 " Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 416.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2640 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 30 sheets defined 22.5% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.658A pdb=" N LEU A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 187 removed outlier: 3.673A pdb=" N LYS A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 382 removed outlier: 3.637A pdb=" N THR A 367 " --> pdb=" O ASP A 363 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 376 " --> pdb=" O ASP A 372 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 377 " --> pdb=" O GLN A 373 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 452 removed outlier: 3.613A pdb=" N VAL A 406 " --> pdb=" O GLN A 402 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A 416 " --> pdb=" O ASP A 412 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 480 removed outlier: 3.596A pdb=" N SER A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 478 " --> pdb=" O CYS A 474 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'B' and resid 95 through 105 removed outlier: 3.657A pdb=" N LEU B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 187 removed outlier: 3.672A pdb=" N LYS B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 382 removed outlier: 3.637A pdb=" N THR B 367 " --> pdb=" O ASP B 363 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 376 " --> pdb=" O ASP B 372 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 377 " --> pdb=" O GLN B 373 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 452 removed outlier: 3.613A pdb=" N VAL B 406 " --> pdb=" O GLN B 402 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU B 416 " --> pdb=" O ASP B 412 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 480 removed outlier: 3.596A pdb=" N SER B 477 " --> pdb=" O ASP B 473 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 478 " --> pdb=" O CYS B 474 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 493 Processing helix chain 'C' and resid 95 through 105 removed outlier: 3.658A pdb=" N LEU C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU C 105 " --> pdb=" O GLN C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 187 removed outlier: 3.673A pdb=" N LYS C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 382 removed outlier: 3.637A pdb=" N THR C 367 " --> pdb=" O ASP C 363 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY C 376 " --> pdb=" O ASP C 372 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS C 377 " --> pdb=" O GLN C 373 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 452 removed outlier: 3.614A pdb=" N VAL C 406 " --> pdb=" O GLN C 402 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU C 416 " --> pdb=" O ASP C 412 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 440 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET C 441 " --> pdb=" O ALA C 437 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 480 removed outlier: 3.597A pdb=" N SER C 477 " --> pdb=" O ASP C 473 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE C 478 " --> pdb=" O CYS C 474 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 Processing sheet with id=1, first strand: chain 'A' and resid 357 through 360 removed outlier: 3.745A pdb=" N GLY A 359 " --> pdb=" O HIS A 352 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 457 " --> pdb=" O GLU A 465 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=3, first strand: chain 'A' and resid 30 through 32 Processing sheet with id=4, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=5, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.700A pdb=" N ILE A 42 " --> pdb=" O ASP A 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=5 Processing sheet with id=6, first strand: chain 'A' and resid 49 through 51 removed outlier: 6.076A pdb=" N ILE A 78 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 91 through 93 removed outlier: 7.002A pdb=" N LYS A 92 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N TRP A 226 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL A 171 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE A 243 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 144 " --> pdb=" O PHE A 243 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 110 through 113 removed outlier: 3.544A pdb=" N GLU A 112 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 156 through 161 Processing sheet with id=10, first strand: chain 'A' and resid 278 through 279 removed outlier: 3.534A pdb=" N GLY A 278 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 357 through 360 removed outlier: 3.745A pdb=" N GLY B 359 " --> pdb=" O HIS B 352 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 457 " --> pdb=" O GLU B 465 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'B' and resid 15 through 17 Processing sheet with id=13, first strand: chain 'B' and resid 30 through 32 Processing sheet with id=14, first strand: chain 'B' and resid 34 through 35 Processing sheet with id=15, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.700A pdb=" N ILE B 42 " --> pdb=" O ASP B 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=15 Processing sheet with id=16, first strand: chain 'B' and resid 49 through 51 removed outlier: 6.076A pdb=" N ILE B 78 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'B' and resid 91 through 93 removed outlier: 7.001A pdb=" N LYS B 92 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N TRP B 226 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL B 171 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE B 243 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 144 " --> pdb=" O PHE B 243 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'B' and resid 110 through 113 removed outlier: 3.544A pdb=" N GLU B 112 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'B' and resid 156 through 161 Processing sheet with id=20, first strand: chain 'B' and resid 278 through 279 removed outlier: 3.534A pdb=" N GLY B 278 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'C' and resid 357 through 360 removed outlier: 3.745A pdb=" N GLY C 359 " --> pdb=" O HIS C 352 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 457 " --> pdb=" O GLU C 465 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'C' and resid 15 through 17 Processing sheet with id=23, first strand: chain 'C' and resid 30 through 32 Processing sheet with id=24, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=25, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.700A pdb=" N ILE C 42 " --> pdb=" O ASP C 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=25 Processing sheet with id=26, first strand: chain 'C' and resid 49 through 51 removed outlier: 6.075A pdb=" N ILE C 78 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'C' and resid 91 through 93 removed outlier: 7.001A pdb=" N LYS C 92 " --> pdb=" O PHE C 224 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N TRP C 226 " --> pdb=" O LYS C 92 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL C 171 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE C 243 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 144 " --> pdb=" O PHE C 243 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'C' and resid 110 through 113 removed outlier: 3.544A pdb=" N GLU C 112 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'C' and resid 156 through 161 Processing sheet with id=30, first strand: chain 'C' and resid 278 through 279 removed outlier: 3.534A pdb=" N GLY C 278 " --> pdb=" O HIS C 275 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 981 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: 1.70 Time building geometry restraints manager: 1.28 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: 3904 1.34 - 1.46: 2648 1.46 - 1.58: 5040 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 11682 Sorted by residual: bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" C1 NAG C 503 " pdb=" O5 NAG C 503 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.17e+00 bond pdb=" C1 NAG B 503 " pdb=" O5 NAG B 503 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" CA GLY B 53 " pdb=" C GLY B 53 " ideal model delta sigma weight residual 1.530 1.511 0.020 1.04e-02 9.25e+03 3.70e+00 bond pdb=" CA GLY A 53 " pdb=" C GLY A 53 " ideal model delta sigma weight residual 1.530 1.511 0.020 1.04e-02 9.25e+03 3.66e+00 ... (remaining 11677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 15136 2.07 - 4.13: 535 4.13 - 6.20: 79 6.20 - 8.26: 15 8.26 - 10.33: 15 Bond angle restraints: 15780 Sorted by residual: angle pdb=" C VAL B 215 " pdb=" N ASN B 216 " pdb=" CA ASN B 216 " ideal model delta sigma weight residual 121.54 130.93 -9.39 1.91e+00 2.74e-01 2.42e+01 angle pdb=" C VAL A 215 " pdb=" N ASN A 216 " pdb=" CA ASN A 216 " ideal model delta sigma weight residual 121.54 130.90 -9.36 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C VAL C 215 " pdb=" N ASN C 216 " pdb=" CA ASN C 216 " ideal model delta sigma weight residual 121.54 130.90 -9.36 1.91e+00 2.74e-01 2.40e+01 angle pdb=" N GLY B 349 " pdb=" CA GLY B 349 " pdb=" C GLY B 349 " ideal model delta sigma weight residual 110.66 118.04 -7.38 1.90e+00 2.77e-01 1.51e+01 angle pdb=" N GLY A 349 " pdb=" CA GLY A 349 " pdb=" C GLY A 349 " ideal model delta sigma weight residual 110.66 118.02 -7.36 1.90e+00 2.77e-01 1.50e+01 ... (remaining 15775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.88: 6679 15.88 - 31.76: 332 31.76 - 47.63: 93 47.63 - 63.51: 30 63.51 - 79.39: 15 Dihedral angle restraints: 7149 sinusoidal: 3021 harmonic: 4128 Sorted by residual: dihedral pdb=" CA ASN B 397 " pdb=" C ASN B 397 " pdb=" N GLU B 398 " pdb=" CA GLU B 398 " ideal model delta harmonic sigma weight residual 180.00 134.08 45.92 0 5.00e+00 4.00e-02 8.43e+01 dihedral pdb=" CA ASN A 397 " pdb=" C ASN A 397 " pdb=" N GLU A 398 " pdb=" CA GLU A 398 " ideal model delta harmonic sigma weight residual 180.00 134.11 45.89 0 5.00e+00 4.00e-02 8.42e+01 dihedral pdb=" CA ASN C 397 " pdb=" C ASN C 397 " pdb=" N GLU C 398 " pdb=" CA GLU C 398 " ideal model delta harmonic sigma weight residual 180.00 134.13 45.87 0 5.00e+00 4.00e-02 8.42e+01 ... (remaining 7146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1373 0.066 - 0.132: 296 0.132 - 0.198: 38 0.198 - 0.264: 14 0.264 - 0.330: 7 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CB ILE B 281 " pdb=" CA ILE B 281 " pdb=" CG1 ILE B 281 " pdb=" CG2 ILE B 281 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB ILE A 281 " pdb=" CA ILE A 281 " pdb=" CG1 ILE A 281 " pdb=" CG2 ILE A 281 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB ILE C 281 " pdb=" CA ILE C 281 " pdb=" CG1 ILE C 281 " pdb=" CG2 ILE C 281 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 1725 not shown) Planarity restraints: 2094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 143 " -0.025 2.00e-02 2.50e+03 1.76e-02 7.76e+00 pdb=" CG TRP B 143 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP B 143 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 143 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 143 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 143 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 143 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 143 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 143 " 0.024 2.00e-02 2.50e+03 1.76e-02 7.73e+00 pdb=" CG TRP A 143 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 143 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 143 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 143 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 143 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 143 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 143 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 143 " -0.024 2.00e-02 2.50e+03 1.75e-02 7.69e+00 pdb=" CG TRP C 143 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 143 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP C 143 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 143 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 143 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 143 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 143 " -0.006 2.00e-02 2.50e+03 ... (remaining 2091 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.28: 9 2.28 - 2.93: 4636 2.93 - 3.59: 14772 3.59 - 4.24: 25585 4.24 - 4.90: 42760 Nonbonded interactions: 87762 Sorted by model distance: nonbonded pdb=" NH2 ARG A 453 " pdb=" OE1 GLU B 457 " model vdw 1.625 3.120 nonbonded pdb=" OE1 GLU A 457 " pdb=" NH2 ARG C 453 " model vdw 1.625 3.120 nonbonded pdb=" NH2 ARG B 453 " pdb=" OE1 GLU C 457 " model vdw 1.625 3.120 nonbonded pdb=" NH2 ARG A 212 " pdb=" NE2 GLN C 202 " model vdw 2.083 3.200 nonbonded pdb=" NE2 GLN A 202 " pdb=" NH2 ARG B 212 " model vdw 2.084 3.200 ... (remaining 87757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.880 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.950 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6132 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 0.058 11709 Z= 0.271 Angle : 0.968 13.496 15843 Z= 0.521 Chirality : 0.061 0.330 1728 Planarity : 0.005 0.048 2085 Dihedral : 11.603 79.385 4455 Min Nonbonded Distance : 1.625 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.49 % Allowed : 4.15 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.55 (0.16), residues: 1440 helix: -4.69 (0.09), residues: 297 sheet: -2.14 (0.27), residues: 336 loop : -2.78 (0.16), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 164 TYR 0.028 0.003 TYR B 274 PHE 0.040 0.005 PHE B 251 TRP 0.046 0.004 TRP B 143 HIS 0.010 0.002 HIS C 468 Details of bonding type rmsd covalent geometry : bond 0.00596 (11682) covalent geometry : angle 0.94284 (15780) SS BOND : bond 0.00315 ( 18) SS BOND : angle 1.39769 ( 36) hydrogen bonds : bond 0.32043 ( 354) hydrogen bonds : angle 9.78013 ( 981) link_NAG-ASN : bond 0.00620 ( 9) link_NAG-ASN : angle 5.31373 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 339 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: B 382 ILE cc_start: 0.6813 (mm) cc_final: 0.6541 (pt) REVERT: C 407 ILE cc_start: 0.5486 (mt) cc_final: 0.5233 (mt) outliers start: 6 outliers final: 1 residues processed: 343 average time/residue: 0.1194 time to fit residues: 55.8991 Evaluate side-chains 161 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 147 ASN A 202 GLN ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN B 8 HIS B 288 ASN ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN C 8 HIS C 13 ASN C 95 ASN C 147 ASN C 175 HIS C 264 GLN C 288 ASN C 394 ASN C 451 GLN C 455 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.155459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137945 restraints weight = 16177.511| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.38 r_work: 0.3612 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.6113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11709 Z= 0.203 Angle : 0.832 11.199 15843 Z= 0.424 Chirality : 0.051 0.462 1728 Planarity : 0.006 0.057 2085 Dihedral : 7.834 58.431 1766 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.74 % Allowed : 9.19 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.17 (0.18), residues: 1440 helix: -2.13 (0.26), residues: 276 sheet: -1.61 (0.28), residues: 327 loop : -2.36 (0.17), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 479 TYR 0.013 0.002 TYR C 201 PHE 0.026 0.003 PHE C 205 TRP 0.037 0.003 TRP C 143 HIS 0.007 0.002 HIS B 9 Details of bonding type rmsd covalent geometry : bond 0.00431 (11682) covalent geometry : angle 0.81239 (15780) SS BOND : bond 0.01126 ( 18) SS BOND : angle 1.86335 ( 36) hydrogen bonds : bond 0.06033 ( 354) hydrogen bonds : angle 5.46065 ( 981) link_NAG-ASN : bond 0.00498 ( 9) link_NAG-ASN : angle 3.98174 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 209 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 GLN cc_start: 0.8620 (tt0) cc_final: 0.8395 (tt0) REVERT: A 454 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7234 (tm-30) REVERT: A 493 MET cc_start: 0.6193 (mtt) cc_final: 0.5986 (mmm) REVERT: B 441 MET cc_start: 0.7900 (tpt) cc_final: 0.7671 (tpt) REVERT: B 493 MET cc_start: 0.6728 (tpp) cc_final: 0.6453 (mmm) REVERT: C 222 ILE cc_start: 0.7626 (mt) cc_final: 0.7170 (mt) REVERT: C 371 ILE cc_start: 0.8511 (pt) cc_final: 0.8307 (pt) REVERT: C 378 LEU cc_start: 0.7889 (mp) cc_final: 0.7644 (tt) REVERT: C 412 ASP cc_start: 0.7803 (m-30) cc_final: 0.7469 (m-30) outliers start: 46 outliers final: 19 residues processed: 247 average time/residue: 0.1152 time to fit residues: 39.5286 Evaluate side-chains 141 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 234 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 127 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 49 optimal weight: 0.0770 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 126 optimal weight: 0.3980 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN B 352 HIS B 432 HIS B 451 GLN ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 GLN C 356 GLN C 368 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.142126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.123509 restraints weight = 16109.972| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.36 r_work: 0.3425 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.7477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11709 Z= 0.148 Angle : 0.646 11.704 15843 Z= 0.330 Chirality : 0.049 0.583 1728 Planarity : 0.004 0.034 2085 Dihedral : 6.842 56.249 1764 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.58 % Allowed : 11.95 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.24 (0.19), residues: 1440 helix: -0.27 (0.30), residues: 294 sheet: -1.19 (0.27), residues: 342 loop : -2.15 (0.17), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 248 TYR 0.022 0.001 TYR B 364 PHE 0.015 0.002 PHE C 396 TRP 0.031 0.001 TRP B 143 HIS 0.005 0.001 HIS B 9 Details of bonding type rmsd covalent geometry : bond 0.00326 (11682) covalent geometry : angle 0.62059 (15780) SS BOND : bond 0.00544 ( 18) SS BOND : angle 1.57142 ( 36) hydrogen bonds : bond 0.06380 ( 354) hydrogen bonds : angle 4.40275 ( 981) link_NAG-ASN : bond 0.00600 ( 9) link_NAG-ASN : angle 4.04990 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7505 (tm-30) REVERT: A 493 MET cc_start: 0.6705 (mtt) cc_final: 0.6335 (mmm) REVERT: B 105 GLU cc_start: 0.7998 (pp20) cc_final: 0.7744 (pp20) REVERT: B 372 ASP cc_start: 0.8063 (t70) cc_final: 0.7659 (m-30) REVERT: B 412 ASP cc_start: 0.8526 (p0) cc_final: 0.8309 (m-30) REVERT: B 428 MET cc_start: 0.8175 (ttp) cc_final: 0.7950 (mtp) REVERT: B 493 MET cc_start: 0.7581 (tpp) cc_final: 0.7263 (mmm) REVERT: C 54 GLN cc_start: 0.7113 (pm20) cc_final: 0.6870 (mm-40) REVERT: C 105 GLU cc_start: 0.8420 (pp20) cc_final: 0.8153 (pp20) REVERT: C 222 ILE cc_start: 0.7996 (mt) cc_final: 0.7626 (mt) REVERT: C 240 ASN cc_start: 0.7531 (OUTLIER) cc_final: 0.6868 (t0) REVERT: C 412 ASP cc_start: 0.8353 (m-30) cc_final: 0.8080 (m-30) outliers start: 44 outliers final: 25 residues processed: 186 average time/residue: 0.1011 time to fit residues: 27.0366 Evaluate side-chains 141 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 444 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 119 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 HIS B 150 ASN B 264 GLN B 288 ASN C 202 GLN C 264 GLN C 288 ASN C 338 ASN C 352 HIS C 356 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.126558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.107614 restraints weight = 16335.543| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.36 r_work: 0.3204 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.9584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.091 11709 Z= 0.363 Angle : 0.881 11.675 15843 Z= 0.444 Chirality : 0.057 0.476 1728 Planarity : 0.005 0.035 2085 Dihedral : 8.199 59.775 1764 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.85 % Allowed : 11.79 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -2.28 (0.19), residues: 1440 helix: -0.21 (0.30), residues: 294 sheet: -1.20 (0.27), residues: 342 loop : -2.22 (0.17), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 351 TYR 0.021 0.003 TYR C 187 PHE 0.031 0.004 PHE B 251 TRP 0.015 0.002 TRP C 226 HIS 0.014 0.002 HIS B 9 Details of bonding type rmsd covalent geometry : bond 0.00890 (11682) covalent geometry : angle 0.85821 (15780) SS BOND : bond 0.00842 ( 18) SS BOND : angle 2.10184 ( 36) hydrogen bonds : bond 0.07932 ( 354) hydrogen bonds : angle 4.65731 ( 981) link_NAG-ASN : bond 0.00622 ( 9) link_NAG-ASN : angle 4.40672 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 134 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 ASN cc_start: 0.8448 (m-40) cc_final: 0.8065 (m-40) REVERT: A 454 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7618 (tm-30) REVERT: A 493 MET cc_start: 0.7118 (mtt) cc_final: 0.6501 (mmm) REVERT: B 122 ARG cc_start: 0.7931 (ptp90) cc_final: 0.7709 (ptp-170) REVERT: B 373 GLN cc_start: 0.8903 (mt0) cc_final: 0.8698 (mt0) REVERT: B 428 MET cc_start: 0.8313 (ttp) cc_final: 0.8087 (mtp) REVERT: B 441 MET cc_start: 0.8937 (tpt) cc_final: 0.8556 (tpt) REVERT: B 493 MET cc_start: 0.8010 (tpp) cc_final: 0.7557 (mmm) REVERT: C 54 GLN cc_start: 0.7733 (pm20) cc_final: 0.7508 (mm-40) REVERT: C 78 ILE cc_start: 0.9099 (pt) cc_final: 0.8851 (mt) REVERT: C 105 GLU cc_start: 0.8628 (pp20) cc_final: 0.8426 (pp20) REVERT: C 131 ARG cc_start: 0.8020 (mmm-85) cc_final: 0.7614 (mtp85) REVERT: C 156 MET cc_start: 0.7824 (mmt) cc_final: 0.7619 (mpp) REVERT: C 287 GLN cc_start: 0.9333 (OUTLIER) cc_final: 0.8198 (pm20) REVERT: C 444 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8927 (tp) outliers start: 72 outliers final: 48 residues processed: 186 average time/residue: 0.0981 time to fit residues: 26.5875 Evaluate side-chains 153 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 103 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 444 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 40 optimal weight: 0.5980 chunk 136 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 GLN C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.130781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112722 restraints weight = 16002.942| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.27 r_work: 0.3283 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.9682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11709 Z= 0.136 Angle : 0.633 12.581 15843 Z= 0.319 Chirality : 0.048 0.535 1728 Planarity : 0.003 0.031 2085 Dihedral : 7.155 58.285 1764 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.07 % Allowed : 15.20 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.69 (0.20), residues: 1440 helix: 0.56 (0.30), residues: 294 sheet: -0.89 (0.28), residues: 327 loop : -1.92 (0.18), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 486 TYR 0.021 0.001 TYR B 187 PHE 0.013 0.001 PHE C 335 TRP 0.009 0.001 TRP C 409 HIS 0.004 0.001 HIS B 9 Details of bonding type rmsd covalent geometry : bond 0.00311 (11682) covalent geometry : angle 0.59753 (15780) SS BOND : bond 0.00552 ( 18) SS BOND : angle 1.77928 ( 36) hydrogen bonds : bond 0.05899 ( 354) hydrogen bonds : angle 4.28120 ( 981) link_NAG-ASN : bond 0.00675 ( 9) link_NAG-ASN : angle 4.73738 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 121 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8151 (pp) cc_final: 0.7936 (pp) REVERT: A 268 ASN cc_start: 0.8511 (m-40) cc_final: 0.8187 (m-40) REVERT: A 389 PHE cc_start: 0.8563 (m-10) cc_final: 0.8197 (m-10) REVERT: A 444 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8991 (tp) REVERT: B 105 GLU cc_start: 0.8321 (pp20) cc_final: 0.7833 (pm20) REVERT: B 122 ARG cc_start: 0.7718 (ptp90) cc_final: 0.7472 (ptp-170) REVERT: B 372 ASP cc_start: 0.8477 (t70) cc_final: 0.8194 (m-30) REVERT: B 428 MET cc_start: 0.8379 (ttp) cc_final: 0.8121 (mtp) REVERT: B 493 MET cc_start: 0.7925 (tpp) cc_final: 0.7473 (mmm) REVERT: C 6 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8306 (pp) REVERT: C 131 ARG cc_start: 0.7976 (mmm-85) cc_final: 0.7559 (mtp85) REVERT: C 156 MET cc_start: 0.7724 (mmt) cc_final: 0.7325 (mpp) REVERT: C 230 ASN cc_start: 0.7964 (m-40) cc_final: 0.7522 (m-40) REVERT: C 296 LYS cc_start: 0.8436 (mttt) cc_final: 0.8052 (mptt) REVERT: C 428 MET cc_start: 0.8342 (ttm) cc_final: 0.8109 (mtp) REVERT: C 444 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8874 (tp) outliers start: 50 outliers final: 35 residues processed: 155 average time/residue: 0.0916 time to fit residues: 20.8817 Evaluate side-chains 143 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 444 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 76 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 HIS C 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.130136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111276 restraints weight = 16074.466| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.36 r_work: 0.3241 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.9797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11709 Z= 0.160 Angle : 0.649 11.558 15843 Z= 0.326 Chirality : 0.049 0.493 1728 Planarity : 0.003 0.029 2085 Dihedral : 7.131 57.788 1764 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.15 % Allowed : 15.37 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.40 (0.20), residues: 1440 helix: 0.98 (0.30), residues: 294 sheet: -0.68 (0.28), residues: 327 loop : -1.82 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 486 TYR 0.023 0.002 TYR B 364 PHE 0.013 0.002 PHE C 335 TRP 0.009 0.001 TRP C 409 HIS 0.005 0.001 HIS B 9 Details of bonding type rmsd covalent geometry : bond 0.00381 (11682) covalent geometry : angle 0.61706 (15780) SS BOND : bond 0.00562 ( 18) SS BOND : angle 1.84303 ( 36) hydrogen bonds : bond 0.06018 ( 354) hydrogen bonds : angle 4.23498 ( 981) link_NAG-ASN : bond 0.00657 ( 9) link_NAG-ASN : angle 4.45816 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 107 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 ASN cc_start: 0.8396 (m-40) cc_final: 0.8040 (m-40) REVERT: A 444 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8976 (tp) REVERT: B 105 GLU cc_start: 0.8310 (pp20) cc_final: 0.7995 (pm20) REVERT: B 122 ARG cc_start: 0.7929 (ptp90) cc_final: 0.7559 (ptp-170) REVERT: B 372 ASP cc_start: 0.8457 (t70) cc_final: 0.8124 (m-30) REVERT: B 428 MET cc_start: 0.8398 (ttp) cc_final: 0.8057 (mtp) REVERT: B 493 MET cc_start: 0.7938 (tpp) cc_final: 0.7529 (mmm) REVERT: C 6 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8391 (pp) REVERT: C 131 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7533 (mtp85) REVERT: C 156 MET cc_start: 0.7630 (mmt) cc_final: 0.7388 (mpp) REVERT: C 230 ASN cc_start: 0.8006 (m-40) cc_final: 0.7550 (m-40) REVERT: C 296 LYS cc_start: 0.8511 (mttt) cc_final: 0.8101 (mptt) REVERT: C 428 MET cc_start: 0.8374 (ttm) cc_final: 0.8098 (mtp) REVERT: C 444 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8806 (tp) REVERT: C 493 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7364 (mmm) outliers start: 51 outliers final: 41 residues processed: 147 average time/residue: 0.0757 time to fit residues: 16.7682 Evaluate side-chains 147 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 102 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 493 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 45 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 240 ASN C 288 ASN C 405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.130342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112458 restraints weight = 15968.608| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.25 r_work: 0.3251 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.9878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11709 Z= 0.164 Angle : 0.635 11.549 15843 Z= 0.320 Chirality : 0.048 0.449 1728 Planarity : 0.003 0.029 2085 Dihedral : 7.050 57.963 1764 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.39 % Allowed : 15.28 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.25 (0.21), residues: 1440 helix: 1.20 (0.30), residues: 294 sheet: -0.63 (0.28), residues: 327 loop : -1.75 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 486 TYR 0.023 0.002 TYR B 364 PHE 0.013 0.002 PHE A 335 TRP 0.010 0.001 TRP C 409 HIS 0.005 0.001 HIS B 9 Details of bonding type rmsd covalent geometry : bond 0.00395 (11682) covalent geometry : angle 0.60114 (15780) SS BOND : bond 0.00512 ( 18) SS BOND : angle 2.05381 ( 36) hydrogen bonds : bond 0.05987 ( 354) hydrogen bonds : angle 4.19240 ( 981) link_NAG-ASN : bond 0.00605 ( 9) link_NAG-ASN : angle 4.41881 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 111 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8346 (pp) REVERT: A 268 ASN cc_start: 0.8377 (m-40) cc_final: 0.8020 (m-40) REVERT: A 389 PHE cc_start: 0.8600 (m-80) cc_final: 0.8294 (m-80) REVERT: A 444 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8989 (tp) REVERT: B 105 GLU cc_start: 0.8294 (pp20) cc_final: 0.8004 (pm20) REVERT: B 122 ARG cc_start: 0.8000 (ptp90) cc_final: 0.7498 (ptt180) REVERT: B 372 ASP cc_start: 0.8482 (t70) cc_final: 0.8182 (m-30) REVERT: B 428 MET cc_start: 0.8412 (ttp) cc_final: 0.8145 (mtp) REVERT: B 493 MET cc_start: 0.7902 (tpp) cc_final: 0.7666 (mmm) REVERT: C 6 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8317 (pp) REVERT: C 131 ARG cc_start: 0.7919 (mmm-85) cc_final: 0.7503 (mtp85) REVERT: C 230 ASN cc_start: 0.7977 (m-40) cc_final: 0.7529 (m-40) REVERT: C 268 ASN cc_start: 0.8015 (m-40) cc_final: 0.7761 (m-40) REVERT: C 296 LYS cc_start: 0.8528 (mttt) cc_final: 0.8053 (mmtm) REVERT: C 444 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8787 (tp) REVERT: C 493 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7410 (mmm) outliers start: 54 outliers final: 45 residues processed: 151 average time/residue: 0.0898 time to fit residues: 20.1595 Evaluate side-chains 156 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 106 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 493 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 8 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 99 optimal weight: 0.0570 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 ASN C 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112482 restraints weight = 15853.866| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.27 r_work: 0.3275 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.9976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11709 Z= 0.130 Angle : 0.587 11.565 15843 Z= 0.297 Chirality : 0.046 0.413 1728 Planarity : 0.003 0.029 2085 Dihedral : 6.712 59.911 1764 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.07 % Allowed : 16.02 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.99 (0.21), residues: 1440 helix: 1.57 (0.30), residues: 297 sheet: -0.41 (0.30), residues: 312 loop : -1.67 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 486 TYR 0.024 0.001 TYR B 364 PHE 0.013 0.001 PHE A 335 TRP 0.009 0.001 TRP C 409 HIS 0.004 0.001 HIS B 9 Details of bonding type rmsd covalent geometry : bond 0.00304 (11682) covalent geometry : angle 0.55358 (15780) SS BOND : bond 0.00525 ( 18) SS BOND : angle 1.92566 ( 36) hydrogen bonds : bond 0.05530 ( 354) hydrogen bonds : angle 4.08263 ( 981) link_NAG-ASN : bond 0.00752 ( 9) link_NAG-ASN : angle 4.23958 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 112 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8351 (pp) REVERT: A 268 ASN cc_start: 0.8353 (m-40) cc_final: 0.8034 (m-40) REVERT: A 389 PHE cc_start: 0.8639 (m-80) cc_final: 0.8261 (m-80) REVERT: A 444 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8954 (tp) REVERT: B 122 ARG cc_start: 0.8025 (ptp90) cc_final: 0.7514 (ptt180) REVERT: B 372 ASP cc_start: 0.8447 (t70) cc_final: 0.8139 (m-30) REVERT: B 428 MET cc_start: 0.8375 (ttp) cc_final: 0.8082 (mtp) REVERT: B 493 MET cc_start: 0.7834 (tpp) cc_final: 0.7604 (mmm) REVERT: C 6 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8343 (pp) REVERT: C 131 ARG cc_start: 0.7895 (mmm-85) cc_final: 0.7476 (mtp85) REVERT: C 268 ASN cc_start: 0.8045 (m-40) cc_final: 0.7782 (m-40) REVERT: C 296 LYS cc_start: 0.8505 (mttt) cc_final: 0.8039 (mmtm) REVERT: C 428 MET cc_start: 0.8223 (ttm) cc_final: 0.8017 (mtp) REVERT: C 444 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8811 (tp) REVERT: C 493 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7384 (mmm) outliers start: 50 outliers final: 41 residues processed: 144 average time/residue: 0.1028 time to fit residues: 21.6176 Evaluate side-chains 151 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 105 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 493 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 65 optimal weight: 2.9990 chunk 67 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 116 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 ASN C 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.131380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112711 restraints weight = 15918.148| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.35 r_work: 0.3271 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 1.0020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11709 Z= 0.131 Angle : 0.588 11.285 15843 Z= 0.299 Chirality : 0.047 0.401 1728 Planarity : 0.003 0.040 2085 Dihedral : 6.632 59.646 1764 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.15 % Allowed : 15.85 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.21), residues: 1440 helix: 1.83 (0.30), residues: 297 sheet: -0.34 (0.30), residues: 312 loop : -1.61 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 486 TYR 0.022 0.001 TYR B 364 PHE 0.012 0.001 PHE A 335 TRP 0.009 0.001 TRP C 409 HIS 0.003 0.001 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00304 (11682) covalent geometry : angle 0.55692 (15780) SS BOND : bond 0.00508 ( 18) SS BOND : angle 1.83627 ( 36) hydrogen bonds : bond 0.05498 ( 354) hydrogen bonds : angle 4.05930 ( 981) link_NAG-ASN : bond 0.00800 ( 9) link_NAG-ASN : angle 4.11273 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 108 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8381 (pp) REVERT: A 268 ASN cc_start: 0.8355 (m-40) cc_final: 0.8027 (m-40) REVERT: A 444 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8950 (tp) REVERT: B 122 ARG cc_start: 0.8015 (ptp90) cc_final: 0.7452 (ptt180) REVERT: B 240 ASN cc_start: 0.8622 (p0) cc_final: 0.8317 (p0) REVERT: B 372 ASP cc_start: 0.8470 (t70) cc_final: 0.8226 (m-30) REVERT: B 428 MET cc_start: 0.8420 (ttp) cc_final: 0.8117 (mtp) REVERT: C 6 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8370 (pp) REVERT: C 131 ARG cc_start: 0.7878 (mmm-85) cc_final: 0.7513 (mtp85) REVERT: C 182 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7068 (mt-10) REVERT: C 268 ASN cc_start: 0.8175 (m-40) cc_final: 0.7915 (m-40) REVERT: C 296 LYS cc_start: 0.8508 (mttt) cc_final: 0.8039 (mmtm) REVERT: C 428 MET cc_start: 0.8293 (ttm) cc_final: 0.8062 (mtp) REVERT: C 444 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8748 (tp) REVERT: C 493 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7271 (mmm) outliers start: 51 outliers final: 44 residues processed: 141 average time/residue: 0.0940 time to fit residues: 19.4774 Evaluate side-chains 152 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 103 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 493 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 82 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 GLN B 232 ASN C 232 ASN C 264 GLN C 288 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.129461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110643 restraints weight = 16094.226| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.36 r_work: 0.3242 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 1.0055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11709 Z= 0.172 Angle : 0.626 11.182 15843 Z= 0.318 Chirality : 0.048 0.389 1728 Planarity : 0.003 0.040 2085 Dihedral : 6.852 59.553 1764 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.39 % Allowed : 15.61 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.89 (0.21), residues: 1440 helix: 1.80 (0.30), residues: 294 sheet: -0.48 (0.29), residues: 327 loop : -1.61 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 486 TYR 0.022 0.002 TYR B 364 PHE 0.013 0.002 PHE A 116 TRP 0.009 0.001 TRP C 409 HIS 0.005 0.001 HIS B 9 Details of bonding type rmsd covalent geometry : bond 0.00413 (11682) covalent geometry : angle 0.59719 (15780) SS BOND : bond 0.00548 ( 18) SS BOND : angle 1.85560 ( 36) hydrogen bonds : bond 0.05974 ( 354) hydrogen bonds : angle 4.11584 ( 981) link_NAG-ASN : bond 0.00745 ( 9) link_NAG-ASN : angle 4.09566 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 105 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8397 (pp) REVERT: A 268 ASN cc_start: 0.8370 (m-40) cc_final: 0.8024 (m-40) REVERT: A 444 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8965 (tp) REVERT: A 454 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7182 (tm-30) REVERT: A 493 MET cc_start: 0.6980 (mtt) cc_final: 0.6394 (mmm) REVERT: B 122 ARG cc_start: 0.8052 (ptp90) cc_final: 0.7434 (ptt180) REVERT: B 240 ASN cc_start: 0.8621 (p0) cc_final: 0.8303 (p0) REVERT: B 372 ASP cc_start: 0.8467 (t70) cc_final: 0.8229 (m-30) REVERT: B 428 MET cc_start: 0.8417 (ttp) cc_final: 0.8109 (mtp) REVERT: C 6 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8397 (pp) REVERT: C 131 ARG cc_start: 0.7884 (mmm-85) cc_final: 0.7515 (mtp85) REVERT: C 182 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7110 (mt-10) REVERT: C 268 ASN cc_start: 0.8212 (m-40) cc_final: 0.7986 (m-40) REVERT: C 296 LYS cc_start: 0.8480 (mttt) cc_final: 0.8011 (mmtm) REVERT: C 428 MET cc_start: 0.8304 (ttm) cc_final: 0.8095 (mtp) REVERT: C 493 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7319 (mmm) REVERT: C 494 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7679 (mp10) outliers start: 54 outliers final: 48 residues processed: 142 average time/residue: 0.0968 time to fit residues: 19.9392 Evaluate side-chains 154 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 102 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 493 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 67 optimal weight: 0.0000 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 ASN C 232 ASN C 264 GLN C 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.132177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113622 restraints weight = 15995.089| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.35 r_work: 0.3267 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 1.0113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11709 Z= 0.121 Angle : 0.576 10.345 15843 Z= 0.294 Chirality : 0.046 0.370 1728 Planarity : 0.003 0.040 2085 Dihedral : 6.582 57.926 1764 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.98 % Allowed : 16.02 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.67 (0.21), residues: 1440 helix: 2.09 (0.31), residues: 297 sheet: -0.40 (0.29), residues: 327 loop : -1.50 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 486 TYR 0.023 0.001 TYR B 364 PHE 0.012 0.001 PHE C 335 TRP 0.010 0.001 TRP C 409 HIS 0.003 0.001 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00274 (11682) covalent geometry : angle 0.54814 (15780) SS BOND : bond 0.00453 ( 18) SS BOND : angle 1.70283 ( 36) hydrogen bonds : bond 0.05321 ( 354) hydrogen bonds : angle 4.04207 ( 981) link_NAG-ASN : bond 0.00652 ( 9) link_NAG-ASN : angle 3.89380 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2362.72 seconds wall clock time: 41 minutes 23.25 seconds (2483.25 seconds total)