Starting phenix.real_space_refine on Wed May 14 05:47:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iux_35729/05_2025/8iux_35729.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iux_35729/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8iux_35729/05_2025/8iux_35729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iux_35729/05_2025/8iux_35729.map" model { file = "/net/cci-nas-00/data/ceres_data/8iux_35729/05_2025/8iux_35729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iux_35729/05_2025/8iux_35729.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B Time building chain proxies: 7.99, per 1000 atoms: 0.70 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 C 5 " - pdb=" SG CYS C 463 " distance=2.03 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 463 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 67 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 67 " distance=2.03 Simple disulfide: pdb=" SG CYS C 88 " - pdb=" SG CYS C 130 " distance=2.03 Simple disulfide: pdb=" SG CYS B 88 " - pdb=" SG CYS B 130 " distance=2.03 Simple disulfide: pdb=" SG CYS C 273 " - pdb=" SG CYS C 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 273 " - pdb=" SG CYS B 297 " distance=2.02 Simple disulfide: pdb=" SG CYS C 470 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 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: 2.63 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.29 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: 3.77 Time building geometry restraints manager: 3.07 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.380 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.820 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.630 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.046 0.004 TRP B 143 HIS 0.010 0.002 HIS C 468 PHE 0.040 0.005 PHE B 251 TYR 0.028 0.003 TYR B 274 ARG 0.008 0.001 ARG B 164 Details of bonding type rmsd link_NAG-ASN : bond 0.00620 ( 9) link_NAG-ASN : angle 5.31373 ( 27) hydrogen bonds : bond 0.32043 ( 354) hydrogen bonds : angle 9.78013 ( 981) SS BOND : bond 0.00315 ( 18) SS BOND : angle 1.39769 ( 36) covalent geometry : bond 0.00596 (11682) covalent geometry : angle 0.94284 (15780) *********************** 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 : 1.956 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: 0.2716 time to fit residues: 126.3556 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 : 1.701 ------------------------------------------------------------------------------- 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 121 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 112 optimal weight: 0.0030 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- 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 202 GLN C 264 GLN C 288 ASN C 338 ASN C 394 ASN C 451 GLN C 455 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.153099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.135336 restraints weight = 16035.622| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.38 r_work: 0.3576 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.6101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11709 Z= 0.201 Angle : 0.843 12.750 15843 Z= 0.428 Chirality : 0.052 0.535 1728 Planarity : 0.006 0.073 2085 Dihedral : 7.821 58.856 1766 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.90 % Allowed : 9.11 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.18), residues: 1440 helix: -2.32 (0.24), residues: 291 sheet: -1.60 (0.27), residues: 342 loop : -2.47 (0.16), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP C 143 HIS 0.007 0.002 HIS B 9 PHE 0.025 0.003 PHE C 205 TYR 0.014 0.002 TYR A 274 ARG 0.014 0.001 ARG C 479 Details of bonding type rmsd link_NAG-ASN : bond 0.00589 ( 9) link_NAG-ASN : angle 3.18996 ( 27) hydrogen bonds : bond 0.06441 ( 354) hydrogen bonds : angle 5.34996 ( 981) SS BOND : bond 0.00790 ( 18) SS BOND : angle 1.72004 ( 36) covalent geometry : bond 0.00438 (11682) covalent geometry : angle 0.83010 (15780) *********************** 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 250 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 202 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7579 (tm-30) REVERT: A 493 MET cc_start: 0.6412 (mtt) cc_final: 0.6201 (mmm) REVERT: B 441 MET cc_start: 0.7957 (tpt) cc_final: 0.7711 (tpt) REVERT: B 493 MET cc_start: 0.6860 (tpp) cc_final: 0.6540 (mmm) REVERT: C 41 ARG cc_start: 0.7701 (ptp-110) cc_final: 0.7483 (mtm110) REVERT: C 222 ILE cc_start: 0.7742 (mt) cc_final: 0.7311 (mt) REVERT: C 371 ILE cc_start: 0.8525 (pt) cc_final: 0.8094 (mt) REVERT: C 378 LEU cc_start: 0.7988 (mp) cc_final: 0.7674 (tt) REVERT: C 412 ASP cc_start: 0.7814 (m-30) cc_final: 0.7493 (m-30) REVERT: C 441 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8056 (tpp) outliers start: 48 outliers final: 17 residues processed: 242 average time/residue: 0.2565 time to fit residues: 85.6952 Evaluate side-chains 130 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 12 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 441 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 451 GLN B 264 GLN B 288 ASN B 352 HIS B 432 HIS B 451 GLN C 264 GLN C 368 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.131784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113558 restraints weight = 16227.739| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.30 r_work: 0.3278 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.8831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 11709 Z= 0.250 Angle : 0.812 11.820 15843 Z= 0.411 Chirality : 0.054 0.543 1728 Planarity : 0.005 0.035 2085 Dihedral : 7.757 59.790 1764 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.80 % Allowed : 11.63 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.19), residues: 1440 helix: -0.77 (0.28), residues: 297 sheet: -1.38 (0.27), residues: 342 loop : -2.30 (0.17), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 143 HIS 0.008 0.002 HIS B 9 PHE 0.023 0.003 PHE A 93 TYR 0.022 0.002 TYR B 364 ARG 0.006 0.001 ARG B 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00826 ( 9) link_NAG-ASN : angle 4.46106 ( 27) hydrogen bonds : bond 0.08061 ( 354) hydrogen bonds : angle 4.73252 ( 981) SS BOND : bond 0.00641 ( 18) SS BOND : angle 2.23921 ( 36) covalent geometry : bond 0.00604 (11682) covalent geometry : angle 0.78533 (15780) *********************** 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 216 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 157 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 CYS cc_start: 0.7535 (m) cc_final: 0.7149 (m) REVERT: A 145 LEU cc_start: 0.8331 (pp) cc_final: 0.8126 (pp) REVERT: A 268 ASN cc_start: 0.8347 (m-40) cc_final: 0.8016 (m-40) REVERT: A 454 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7592 (tm-30) REVERT: A 493 MET cc_start: 0.6994 (mtt) cc_final: 0.6478 (mmm) REVERT: B 78 ILE cc_start: 0.9297 (pt) cc_final: 0.8899 (mt) REVERT: B 105 GLU cc_start: 0.8350 (pp20) cc_final: 0.7906 (pp20) REVERT: B 428 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8194 (mtp) REVERT: B 431 GLN cc_start: 0.8545 (tp40) cc_final: 0.8306 (tp40) REVERT: B 493 MET cc_start: 0.8075 (tpp) cc_final: 0.7584 (mmm) REVERT: B 494 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7275 (mp10) REVERT: C 156 MET cc_start: 0.7605 (mmt) cc_final: 0.6885 (mtm) outliers start: 59 outliers final: 38 residues processed: 199 average time/residue: 0.2281 time to fit residues: 65.1461 Evaluate side-chains 147 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 1.507 ------------------------------------------------------------------------------- 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 57 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 170 ILE 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 381 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 465 GLU 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 140 GLU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 171 VAL 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 398 GLU Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 463 CYS 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 147 ASN Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 436 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 99 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN C 264 GLN C 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.132300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114296 restraints weight = 16096.866| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.27 r_work: 0.3277 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.9168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11709 Z= 0.154 Angle : 0.666 12.639 15843 Z= 0.332 Chirality : 0.049 0.515 1728 Planarity : 0.003 0.032 2085 Dihedral : 7.171 56.600 1764 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.15 % Allowed : 13.41 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.20), residues: 1440 helix: 0.15 (0.30), residues: 294 sheet: -1.06 (0.27), residues: 342 loop : -2.10 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 409 HIS 0.005 0.001 HIS B 9 PHE 0.014 0.002 PHE C 335 TYR 0.018 0.001 TYR B 364 ARG 0.006 0.001 ARG A 486 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 9) link_NAG-ASN : angle 4.65347 ( 27) hydrogen bonds : bond 0.06091 ( 354) hydrogen bonds : angle 4.36806 ( 981) SS BOND : bond 0.00603 ( 18) SS BOND : angle 2.18192 ( 36) covalent geometry : bond 0.00356 (11682) covalent geometry : angle 0.63051 (15780) *********************** 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 164 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 113 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8199 (pp) cc_final: 0.7995 (pp) REVERT: A 268 ASN cc_start: 0.8413 (m-40) cc_final: 0.8109 (m-40) REVERT: B 140 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7182 (pp20) REVERT: B 372 ASP cc_start: 0.8473 (t70) cc_final: 0.8137 (m-30) REVERT: B 412 ASP cc_start: 0.8449 (m-30) cc_final: 0.7994 (m-30) REVERT: B 493 MET cc_start: 0.7942 (tpp) cc_final: 0.7381 (mmm) REVERT: C 131 ARG cc_start: 0.7887 (mmm-85) cc_final: 0.7511 (mtp85) REVERT: C 156 MET cc_start: 0.7634 (mmt) cc_final: 0.7263 (mpp) REVERT: C 296 LYS cc_start: 0.8414 (mttt) cc_final: 0.7969 (mmtm) REVERT: C 444 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8854 (tp) outliers start: 51 outliers final: 36 residues processed: 149 average time/residue: 0.2342 time to fit residues: 50.2485 Evaluate side-chains 133 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 170 ILE 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 465 GLU Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 165 GLU 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 312 MET Chi-restraints excluded: chain B residue 378 LEU 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 C residue 4 ILE Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 12 SER 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 206 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 356 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 41 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 0.0020 chunk 123 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 HIS C 264 GLN C 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.115139 restraints weight = 15961.693| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.34 r_work: 0.3294 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.9346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11709 Z= 0.120 Angle : 0.621 13.600 15843 Z= 0.311 Chirality : 0.047 0.481 1728 Planarity : 0.003 0.029 2085 Dihedral : 6.733 59.598 1764 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.50 % Allowed : 14.07 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.20), residues: 1440 helix: 0.80 (0.31), residues: 294 sheet: -0.83 (0.29), residues: 327 loop : -1.94 (0.18), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 409 HIS 0.003 0.001 HIS B 9 PHE 0.013 0.001 PHE C 335 TYR 0.018 0.001 TYR B 187 ARG 0.006 0.000 ARG C 486 Details of bonding type rmsd link_NAG-ASN : bond 0.00643 ( 9) link_NAG-ASN : angle 4.43848 ( 27) hydrogen bonds : bond 0.05535 ( 354) hydrogen bonds : angle 4.21674 ( 981) SS BOND : bond 0.00551 ( 18) SS BOND : angle 2.78783 ( 36) covalent geometry : bond 0.00264 (11682) covalent geometry : angle 0.57974 (15780) *********************** 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 156 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 113 time to evaluate : 1.497 Fit side-chains revert: symmetry clash REVERT: A 268 ASN cc_start: 0.8312 (m-40) cc_final: 0.8006 (m-40) REVERT: A 389 PHE cc_start: 0.8624 (m-80) cc_final: 0.8322 (m-10) REVERT: B 105 GLU cc_start: 0.8399 (pp20) cc_final: 0.8108 (pm20) REVERT: B 372 ASP cc_start: 0.8482 (t70) cc_final: 0.8164 (m-30) REVERT: B 412 ASP cc_start: 0.8595 (m-30) cc_final: 0.8181 (m-30) REVERT: B 493 MET cc_start: 0.7783 (tpp) cc_final: 0.7544 (mmt) REVERT: C 131 ARG cc_start: 0.7942 (mmm-85) cc_final: 0.7500 (mtp85) REVERT: C 185 LYS cc_start: 0.7694 (tmtt) cc_final: 0.7421 (tmtt) REVERT: C 296 LYS cc_start: 0.8383 (mttt) cc_final: 0.7982 (mptt) REVERT: C 372 ASP cc_start: 0.8456 (t70) cc_final: 0.8169 (m-30) REVERT: C 428 MET cc_start: 0.8322 (ttm) cc_final: 0.8030 (mtp) REVERT: C 444 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8788 (tp) outliers start: 43 outliers final: 36 residues processed: 141 average time/residue: 0.2339 time to fit residues: 47.9668 Evaluate side-chains 138 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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 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 465 GLU Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 165 GLU 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 312 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 4 ILE 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 206 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 475 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 49 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.0040 chunk 62 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.133325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114592 restraints weight = 16062.767| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.36 r_work: 0.3290 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.9533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11709 Z= 0.131 Angle : 0.620 13.404 15843 Z= 0.310 Chirality : 0.048 0.462 1728 Planarity : 0.003 0.029 2085 Dihedral : 6.657 57.869 1764 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.23 % Allowed : 14.39 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.21), residues: 1440 helix: 1.13 (0.30), residues: 297 sheet: -0.68 (0.29), residues: 327 loop : -1.80 (0.18), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 409 HIS 0.003 0.001 HIS B 9 PHE 0.012 0.001 PHE A 335 TYR 0.017 0.001 TYR C 364 ARG 0.006 0.000 ARG C 486 Details of bonding type rmsd link_NAG-ASN : bond 0.00862 ( 9) link_NAG-ASN : angle 4.20276 ( 27) hydrogen bonds : bond 0.05607 ( 354) hydrogen bonds : angle 4.20499 ( 981) SS BOND : bond 0.00526 ( 18) SS BOND : angle 2.77205 ( 36) covalent geometry : bond 0.00302 (11682) covalent geometry : angle 0.58110 (15780) *********************** 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 165 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 113 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 ASN cc_start: 0.8342 (m-40) cc_final: 0.8025 (m-40) REVERT: A 428 MET cc_start: 0.8273 (ttm) cc_final: 0.7901 (mtp) REVERT: B 412 ASP cc_start: 0.8568 (m-30) cc_final: 0.8232 (m-30) REVERT: B 493 MET cc_start: 0.7845 (tpp) cc_final: 0.7604 (mmm) REVERT: C 43 CYS cc_start: 0.7165 (m) cc_final: 0.6945 (m) REVERT: C 131 ARG cc_start: 0.8039 (mmm-85) cc_final: 0.7575 (mtp85) REVERT: C 185 LYS cc_start: 0.7815 (tmtt) cc_final: 0.7550 (tmtt) REVERT: C 296 LYS cc_start: 0.8449 (mttt) cc_final: 0.8039 (mptt) REVERT: C 372 ASP cc_start: 0.8429 (t70) cc_final: 0.8144 (m-30) REVERT: C 428 MET cc_start: 0.8312 (ttm) cc_final: 0.7985 (mtp) REVERT: C 444 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8813 (tp) outliers start: 52 outliers final: 44 residues processed: 147 average time/residue: 0.2396 time to fit residues: 50.8518 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 : 1.193 ------------------------------------------------------------------------------- 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 465 GLU Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 6 LEU 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 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 281 ILE Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 378 LEU 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 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 206 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 GLN 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 475 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 126 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 GLN C 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.131628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112810 restraints weight = 16106.596| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.37 r_work: 0.3267 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.9707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11709 Z= 0.154 Angle : 0.636 13.349 15843 Z= 0.318 Chirality : 0.048 0.430 1728 Planarity : 0.003 0.029 2085 Dihedral : 6.800 59.874 1764 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.72 % Allowed : 14.15 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.21), residues: 1440 helix: 1.39 (0.30), residues: 294 sheet: -0.56 (0.29), residues: 327 loop : -1.74 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 409 HIS 0.005 0.001 HIS B 9 PHE 0.012 0.002 PHE A 335 TYR 0.016 0.001 TYR B 364 ARG 0.006 0.000 ARG C 486 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 9) link_NAG-ASN : angle 4.22970 ( 27) hydrogen bonds : bond 0.05864 ( 354) hydrogen bonds : angle 4.24823 ( 981) SS BOND : bond 0.00507 ( 18) SS BOND : angle 2.82434 ( 36) covalent geometry : bond 0.00361 (11682) covalent geometry : angle 0.59722 (15780) *********************** 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 162 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 104 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 ASN cc_start: 0.8343 (m-40) cc_final: 0.8017 (m-40) REVERT: A 389 PHE cc_start: 0.8608 (m-80) cc_final: 0.8298 (m-80) REVERT: A 428 MET cc_start: 0.8273 (ttm) cc_final: 0.7850 (mtp) REVERT: A 454 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7823 (tm-30) REVERT: A 493 MET cc_start: 0.7049 (mtt) cc_final: 0.6806 (mmt) REVERT: B 493 MET cc_start: 0.7838 (tpp) cc_final: 0.7580 (mmm) REVERT: C 6 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8563 (pp) REVERT: C 131 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.7566 (mtp85) REVERT: C 296 LYS cc_start: 0.8504 (mttt) cc_final: 0.8097 (mptt) REVERT: C 372 ASP cc_start: 0.8421 (t70) cc_final: 0.8113 (m-30) REVERT: C 428 MET cc_start: 0.8273 (ttm) cc_final: 0.7963 (mtp) REVERT: C 444 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8838 (tp) outliers start: 58 outliers final: 47 residues processed: 141 average time/residue: 0.2340 time to fit residues: 48.6921 Evaluate side-chains 149 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 100 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 465 GLU Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 6 LEU 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 78 ILE Chi-restraints excluded: chain B residue 119 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 206 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 378 LEU 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 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 206 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 GLN 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 475 MET 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 67 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 264 GLN C 288 ASN C 394 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.131845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.113126 restraints weight = 15985.122| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.36 r_work: 0.3281 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.9803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11709 Z= 0.136 Angle : 0.617 12.348 15843 Z= 0.309 Chirality : 0.047 0.409 1728 Planarity : 0.003 0.029 2085 Dihedral : 6.720 58.216 1764 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.63 % Allowed : 14.15 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.21), residues: 1440 helix: 1.62 (0.30), residues: 294 sheet: -0.47 (0.29), residues: 327 loop : -1.66 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 409 HIS 0.004 0.001 HIS B 9 PHE 0.012 0.001 PHE A 335 TYR 0.016 0.001 TYR B 364 ARG 0.007 0.000 ARG B 486 Details of bonding type rmsd link_NAG-ASN : bond 0.00610 ( 9) link_NAG-ASN : angle 3.98966 ( 27) hydrogen bonds : bond 0.05698 ( 354) hydrogen bonds : angle 4.24773 ( 981) SS BOND : bond 0.00457 ( 18) SS BOND : angle 2.76387 ( 36) covalent geometry : bond 0.00316 (11682) covalent geometry : angle 0.58067 (15780) *********************** 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 161 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 104 time to evaluate : 1.384 Fit side-chains revert: symmetry clash REVERT: A 268 ASN cc_start: 0.8367 (m-40) cc_final: 0.8054 (m-40) REVERT: A 389 PHE cc_start: 0.8643 (m-80) cc_final: 0.8326 (m-80) REVERT: A 428 MET cc_start: 0.8249 (ttm) cc_final: 0.7843 (mtp) REVERT: A 454 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7804 (tm-30) REVERT: A 493 MET cc_start: 0.7042 (mtt) cc_final: 0.6812 (mmt) REVERT: B 105 GLU cc_start: 0.8501 (pp20) cc_final: 0.8243 (pm20) REVERT: B 372 ASP cc_start: 0.8508 (t70) cc_final: 0.8183 (m-30) REVERT: B 493 MET cc_start: 0.7794 (tpp) cc_final: 0.7558 (mmm) REVERT: C 6 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8407 (pp) REVERT: C 131 ARG cc_start: 0.7981 (mmm-85) cc_final: 0.7523 (mtp85) REVERT: C 296 LYS cc_start: 0.8509 (mttt) cc_final: 0.8116 (mptt) REVERT: C 372 ASP cc_start: 0.8409 (t70) cc_final: 0.8123 (m-30) REVERT: C 428 MET cc_start: 0.8244 (ttm) cc_final: 0.7936 (mtp) REVERT: C 444 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8820 (tp) REVERT: C 493 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7066 (mmm) outliers start: 57 outliers final: 44 residues processed: 138 average time/residue: 0.2294 time to fit residues: 46.4459 Evaluate side-chains 150 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 103 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 375 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 6 LEU 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 78 ILE 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 206 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 312 MET 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 155 GLN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 GLN 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 475 MET 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 5 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.130909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112169 restraints weight = 16077.514| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.36 r_work: 0.3268 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.9885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11709 Z= 0.152 Angle : 0.629 11.901 15843 Z= 0.316 Chirality : 0.047 0.385 1728 Planarity : 0.003 0.037 2085 Dihedral : 6.800 58.246 1764 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.98 % Allowed : 15.12 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.21), residues: 1440 helix: 1.70 (0.30), residues: 294 sheet: -0.45 (0.29), residues: 327 loop : -1.63 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 409 HIS 0.005 0.001 HIS B 9 PHE 0.012 0.001 PHE A 335 TYR 0.016 0.001 TYR B 364 ARG 0.009 0.000 ARG B 486 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 9) link_NAG-ASN : angle 3.91173 ( 27) hydrogen bonds : bond 0.05844 ( 354) hydrogen bonds : angle 4.21957 ( 981) SS BOND : bond 0.00444 ( 18) SS BOND : angle 2.72465 ( 36) covalent geometry : bond 0.00357 (11682) covalent geometry : angle 0.59455 (15780) *********************** 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 152 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 103 time to evaluate : 1.381 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8273 (pp) REVERT: A 268 ASN cc_start: 0.8434 (m-40) cc_final: 0.8096 (m-40) REVERT: A 428 MET cc_start: 0.8312 (ttm) cc_final: 0.7928 (mtp) REVERT: A 454 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7815 (tm-30) REVERT: A 493 MET cc_start: 0.7005 (mtt) cc_final: 0.6773 (mmt) REVERT: B 372 ASP cc_start: 0.8507 (t70) cc_final: 0.8173 (m-30) REVERT: C 6 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8398 (pp) REVERT: C 131 ARG cc_start: 0.7946 (mmm-85) cc_final: 0.7499 (mtp85) REVERT: C 296 LYS cc_start: 0.8493 (mttt) cc_final: 0.8019 (mmtm) REVERT: C 372 ASP cc_start: 0.8409 (t70) cc_final: 0.8128 (m-30) REVERT: C 428 MET cc_start: 0.8270 (ttm) cc_final: 0.7958 (mtp) REVERT: C 444 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8843 (tp) REVERT: C 493 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7051 (mmm) outliers start: 49 outliers final: 43 residues processed: 136 average time/residue: 0.2324 time to fit residues: 45.9564 Evaluate side-chains 147 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 100 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 375 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 436 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 78 ILE 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 206 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 312 MET 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 155 GLN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 GLN 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 475 MET 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 108 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 112 optimal weight: 0.0770 chunk 107 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 C 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.132639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.114098 restraints weight = 15910.740| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.34 r_work: 0.3288 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.9953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11709 Z= 0.119 Angle : 0.593 10.498 15843 Z= 0.299 Chirality : 0.046 0.372 1728 Planarity : 0.003 0.042 2085 Dihedral : 6.564 55.950 1764 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.90 % Allowed : 15.53 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1440 helix: 1.99 (0.30), residues: 294 sheet: -0.27 (0.30), residues: 312 loop : -1.60 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 409 HIS 0.003 0.001 HIS A 468 PHE 0.012 0.001 PHE A 335 TYR 0.016 0.001 TYR B 364 ARG 0.010 0.000 ARG B 486 Details of bonding type rmsd link_NAG-ASN : bond 0.00652 ( 9) link_NAG-ASN : angle 3.85037 ( 27) hydrogen bonds : bond 0.05437 ( 354) hydrogen bonds : angle 4.18708 ( 981) SS BOND : bond 0.00415 ( 18) SS BOND : angle 2.55563 ( 36) covalent geometry : bond 0.00268 (11682) covalent geometry : angle 0.55885 (15780) ********************** 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 153 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 105 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8310 (pp) REVERT: A 268 ASN cc_start: 0.8423 (m-40) cc_final: 0.8088 (m-40) REVERT: A 428 MET cc_start: 0.8196 (ttm) cc_final: 0.7821 (mtp) REVERT: A 454 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7813 (tm-30) REVERT: A 493 MET cc_start: 0.6929 (mtt) cc_final: 0.6715 (mmt) REVERT: B 105 GLU cc_start: 0.8529 (pp20) cc_final: 0.8262 (pm20) REVERT: B 372 ASP cc_start: 0.8460 (t70) cc_final: 0.8141 (m-30) REVERT: C 6 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8339 (pp) REVERT: C 131 ARG cc_start: 0.7916 (mmm-85) cc_final: 0.7465 (mtp85) REVERT: C 296 LYS cc_start: 0.8489 (mttt) cc_final: 0.8025 (mmtm) REVERT: C 372 ASP cc_start: 0.8375 (t70) cc_final: 0.8123 (m-30) REVERT: C 444 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8807 (tp) REVERT: C 493 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7481 (mmm) outliers start: 48 outliers final: 41 residues processed: 137 average time/residue: 0.2344 time to fit residues: 46.8372 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 : 1.240 ------------------------------------------------------------------------------- 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 465 GLU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 57 LEU 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 312 MET 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 155 GLN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 GLN 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 475 MET 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 75 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 0.0670 overall best weight: 0.8720 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.131282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112545 restraints weight = 15961.540| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.36 r_work: 0.3270 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.9989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11709 Z= 0.145 Angle : 0.614 11.045 15843 Z= 0.310 Chirality : 0.047 0.370 1728 Planarity : 0.003 0.042 2085 Dihedral : 6.683 57.504 1764 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.98 % Allowed : 15.45 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.21), residues: 1440 helix: 1.96 (0.30), residues: 294 sheet: -0.39 (0.29), residues: 327 loop : -1.54 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 409 HIS 0.004 0.001 HIS B 9 PHE 0.012 0.001 PHE A 335 TYR 0.016 0.001 TYR B 364 ARG 0.010 0.000 ARG B 486 Details of bonding type rmsd link_NAG-ASN : bond 0.00739 ( 9) link_NAG-ASN : angle 3.81767 ( 27) hydrogen bonds : bond 0.05705 ( 354) hydrogen bonds : angle 4.24059 ( 981) SS BOND : bond 0.00442 ( 18) SS BOND : angle 2.62603 ( 36) covalent geometry : bond 0.00338 (11682) covalent geometry : angle 0.58073 (15780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5463.88 seconds wall clock time: 96 minutes 4.07 seconds (5764.07 seconds total)