Starting phenix.real_space_refine on Sat Nov 16 15:53:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iux_35729/11_2024/8iux_35729.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iux_35729/11_2024/8iux_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iux_35729/11_2024/8iux_35729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iux_35729/11_2024/8iux_35729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iux_35729/11_2024/8iux_35729.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iux_35729/11_2024/8iux_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-5513/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: 8.53, per 1000 atoms: 0.74 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=6, 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 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: 2.36 Conformation dependent library (CDL) restraints added in 1.6 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: 1.48 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: 3.69 Time building geometry restraints manager: 2.85 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: 6661 15.88 - 31.76: 322 31.76 - 47.63: 91 47.63 - 63.51: 24 63.51 - 79.39: 15 Dihedral angle restraints: 7113 sinusoidal: 2985 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 7110 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: 21 2.28 - 2.93: 4636 2.93 - 3.59: 14796 3.59 - 4.24: 25585 4.24 - 4.90: 42760 Nonbonded interactions: 87798 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=" SG CYS B 273 " pdb=" SG CYS B 297 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS C 273 " pdb=" SG CYS C 297 " model vdw 2.025 3.760 ... (remaining 87793 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 6.340 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 29.190 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.600 ------------------------------------------------------------------------------- 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 11682 Z= 0.394 Angle : 0.943 10.326 15780 Z= 0.516 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 *********************** 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 : 1.266 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: 0.2797 time to fit residues: 130.2931 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 : 1.200 ------------------------------------------------------------------------------- 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: 3.9990 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 264 GLN C 288 ASN C 394 ASN C 455 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.6393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11682 Z= 0.298 Angle : 0.802 11.488 15780 Z= 0.419 Chirality : 0.051 0.490 1728 Planarity : 0.006 0.065 2085 Dihedral : 7.819 58.446 1766 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.58 % Allowed : 9.19 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.27 (0.18), residues: 1440 helix: -2.39 (0.24), residues: 291 sheet: -1.60 (0.27), residues: 327 loop : -2.38 (0.17), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP C 143 HIS 0.009 0.002 HIS B 9 PHE 0.024 0.003 PHE C 205 TYR 0.015 0.002 TYR B 348 ARG 0.010 0.001 ARG C 131 *********************** 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 249 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 451 GLN cc_start: 0.8533 (tt0) cc_final: 0.8315 (tt0) REVERT: A 454 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7101 (tm-30) REVERT: B 441 MET cc_start: 0.8083 (tpt) cc_final: 0.7787 (tpt) REVERT: B 493 MET cc_start: 0.6720 (tpp) cc_final: 0.6401 (mmm) REVERT: C 5 CYS cc_start: 0.7077 (m) cc_final: 0.6529 (t) REVERT: C 371 ILE cc_start: 0.8472 (pt) cc_final: 0.8140 (mt) REVERT: C 378 LEU cc_start: 0.7984 (mp) cc_final: 0.7733 (tt) outliers start: 44 outliers final: 17 residues processed: 242 average time/residue: 0.2767 time to fit residues: 92.0793 Evaluate side-chains 131 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain 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 112 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 403 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 116 optimal weight: 0.3980 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN B 432 HIS B 451 GLN B 455 ASN C 264 GLN C 356 GLN C 368 GLN C 451 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.7717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 11682 Z= 0.224 Angle : 0.623 8.303 15780 Z= 0.324 Chirality : 0.047 0.487 1728 Planarity : 0.004 0.042 2085 Dihedral : 8.257 105.153 1764 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.66 % Allowed : 11.71 % Favored : 84.63 % 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: -2.31 (0.19), residues: 1440 helix: -0.34 (0.29), residues: 294 sheet: -1.22 (0.27), residues: 342 loop : -2.20 (0.17), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 226 HIS 0.006 0.001 HIS B 9 PHE 0.014 0.002 PHE C 396 TYR 0.013 0.001 TYR C 187 ARG 0.005 0.001 ARG C 41 *********************** 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 201 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.7594 (ttm) cc_final: 0.7349 (ttp) REVERT: A 475 MET cc_start: 0.8109 (mmt) cc_final: 0.7879 (mmt) REVERT: B 105 GLU cc_start: 0.7674 (pp20) cc_final: 0.7453 (pp20) REVERT: B 493 MET cc_start: 0.7140 (tpp) cc_final: 0.6848 (mmm) REVERT: C 6 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8219 (pp) REVERT: C 240 ASN cc_start: 0.6988 (OUTLIER) cc_final: 0.6738 (t0) REVERT: C 264 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7210 (pp30) REVERT: C 387 GLN cc_start: 0.7807 (tp-100) cc_final: 0.7593 (tp-100) outliers start: 45 outliers final: 25 residues processed: 186 average time/residue: 0.2419 time to fit residues: 64.6593 Evaluate side-chains 142 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 140 GLU 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 465 GLU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 356 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.0010 chunk 98 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.4980 chunk 139 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 overall best weight: 0.6966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN B 352 HIS ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.8498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11682 Z= 0.202 Angle : 0.574 7.611 15780 Z= 0.300 Chirality : 0.046 0.474 1728 Planarity : 0.003 0.030 2085 Dihedral : 8.122 108.841 1764 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.41 % Allowed : 12.93 % Favored : 83.66 % 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: -1.81 (0.20), residues: 1440 helix: 0.46 (0.30), residues: 297 sheet: -1.06 (0.28), residues: 342 loop : -1.97 (0.18), residues: 801 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 0.012 0.002 PHE B 251 TYR 0.013 0.001 TYR C 187 ARG 0.006 0.000 ARG C 486 *********************** 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 163 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: A 475 MET cc_start: 0.8199 (mmt) cc_final: 0.7887 (mmt) REVERT: B 412 ASP cc_start: 0.7252 (m-30) cc_final: 0.6848 (m-30) REVERT: C 6 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8204 (pp) REVERT: C 240 ASN cc_start: 0.7100 (OUTLIER) cc_final: 0.6833 (t0) outliers start: 42 outliers final: 30 residues processed: 152 average time/residue: 0.2368 time to fit residues: 52.4230 Evaluate side-chains 132 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 6 LEU 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 B residue 4 ILE Chi-restraints excluded: chain B residue 150 ASN 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 5 CYS Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 381 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 115 optimal weight: 0.0870 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN B 288 ASN C 264 GLN C 388 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.9396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 11682 Z= 0.373 Angle : 0.706 8.669 15780 Z= 0.359 Chirality : 0.051 0.435 1728 Planarity : 0.004 0.031 2085 Dihedral : 8.764 110.727 1764 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.12 % Allowed : 12.93 % Favored : 81.95 % 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: -1.78 (0.20), residues: 1440 helix: 0.46 (0.30), residues: 294 sheet: -1.01 (0.28), residues: 342 loop : -1.94 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 226 HIS 0.009 0.002 HIS B 9 PHE 0.020 0.003 PHE A 116 TYR 0.018 0.002 TYR B 187 ARG 0.007 0.001 ARG A 486 *********************** 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 177 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 114 time to evaluate : 1.321 Fit side-chains revert: symmetry clash REVERT: B 122 ARG cc_start: 0.7555 (ptp90) cc_final: 0.7296 (ptp-170) REVERT: B 141 MET cc_start: 0.8611 (mtt) cc_final: 0.8306 (mtt) REVERT: B 269 CYS cc_start: 0.6811 (p) cc_final: 0.6012 (p) REVERT: B 412 ASP cc_start: 0.7572 (m-30) cc_final: 0.7281 (m-30) REVERT: C 240 ASN cc_start: 0.7018 (OUTLIER) cc_final: 0.6770 (t0) REVERT: C 257 MET cc_start: 0.7184 (mtm) cc_final: 0.6975 (mtm) REVERT: C 287 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.7808 (pm20) REVERT: C 431 GLN cc_start: 0.8066 (tp40) cc_final: 0.7819 (tp40) REVERT: C 444 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8797 (tp) outliers start: 63 outliers final: 47 residues processed: 160 average time/residue: 0.2796 time to fit residues: 64.6628 Evaluate side-chains 147 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 97 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 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 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 465 GLU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 170 ILE 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 403 ILE 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 5 CYS Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 287 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 GLN C 388 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.9611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11682 Z= 0.221 Angle : 0.585 8.074 15780 Z= 0.301 Chirality : 0.047 0.486 1728 Planarity : 0.003 0.030 2085 Dihedral : 8.229 110.063 1764 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.55 % Allowed : 14.39 % Favored : 81.06 % 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: -1.38 (0.21), residues: 1440 helix: 1.14 (0.30), residues: 294 sheet: -0.84 (0.28), residues: 342 loop : -1.80 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 409 HIS 0.004 0.001 HIS B 9 PHE 0.012 0.001 PHE A 335 TYR 0.015 0.001 TYR C 364 ARG 0.006 0.000 ARG C 486 *********************** 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 161 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 105 time to evaluate : 1.280 Fit side-chains revert: symmetry clash REVERT: A 145 LEU cc_start: 0.7856 (pp) cc_final: 0.7639 (pp) REVERT: A 428 MET cc_start: 0.7489 (ttm) cc_final: 0.7199 (mtp) REVERT: B 122 ARG cc_start: 0.7551 (ptp90) cc_final: 0.7336 (ptp-170) REVERT: C 6 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8309 (pp) REVERT: C 444 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8774 (tp) outliers start: 56 outliers final: 43 residues processed: 146 average time/residue: 0.2747 time to fit residues: 59.5676 Evaluate side-chains 139 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 94 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 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 444 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 157 THR 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 B residue 448 VAL Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 444 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 64 optimal weight: 0.3980 chunk 85 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 GLN C 388 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.9731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11682 Z= 0.243 Angle : 0.596 8.395 15780 Z= 0.307 Chirality : 0.046 0.419 1728 Planarity : 0.003 0.030 2085 Dihedral : 8.254 110.375 1764 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % 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: -1.13 (0.21), residues: 1440 helix: 1.52 (0.30), residues: 291 sheet: -0.68 (0.29), residues: 327 loop : -1.69 (0.19), residues: 822 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 0.013 0.002 PHE A 335 TYR 0.014 0.001 TYR C 364 ARG 0.006 0.001 ARG B 486 *********************** 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: 57 poor density : 105 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 5 CYS cc_start: 0.6157 (m) cc_final: 0.5937 (m) REVERT: A 428 MET cc_start: 0.7487 (ttm) cc_final: 0.7238 (mtp) REVERT: C 6 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8309 (pp) REVERT: C 444 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8752 (tp) outliers start: 57 outliers final: 48 residues processed: 147 average time/residue: 0.2367 time to fit residues: 51.3940 Evaluate side-chains 143 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 93 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 170 ILE 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 463 CYS 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 124 ASN Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 157 THR 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 B residue 448 VAL Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 470 CYS 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 55 optimal weight: 4.9990 chunk 82 optimal weight: 0.0060 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 GLN C 264 GLN C 388 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.9900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11682 Z= 0.367 Angle : 0.679 8.998 15780 Z= 0.348 Chirality : 0.049 0.411 1728 Planarity : 0.004 0.031 2085 Dihedral : 8.649 111.237 1764 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.96 % Allowed : 14.88 % Favored : 80.16 % 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: -1.21 (0.21), residues: 1440 helix: 1.33 (0.30), residues: 291 sheet: -0.76 (0.29), residues: 327 loop : -1.68 (0.19), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 409 HIS 0.007 0.002 HIS B 9 PHE 0.016 0.002 PHE A 116 TYR 0.016 0.002 TYR B 187 ARG 0.007 0.001 ARG C 486 *********************** 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 165 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 104 time to evaluate : 1.350 Fit side-chains revert: symmetry clash REVERT: A 5 CYS cc_start: 0.6061 (m) cc_final: 0.5801 (m) REVERT: C 6 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8361 (pp) REVERT: C 266 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7421 (m-30) REVERT: C 431 GLN cc_start: 0.8073 (tp40) cc_final: 0.7822 (tp40) REVERT: C 444 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8812 (tp) outliers start: 61 outliers final: 52 residues processed: 148 average time/residue: 0.2310 time to fit residues: 49.7845 Evaluate side-chains 148 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 93 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE 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 170 ILE 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 463 CYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 170 ILE 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 B residue 448 VAL Chi-restraints excluded: chain C residue 5 CYS 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 203 GLN Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 282 SER 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 470 CYS 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 132 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 GLN C 388 GLN C 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.9971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11682 Z= 0.197 Angle : 0.578 8.375 15780 Z= 0.299 Chirality : 0.046 0.418 1728 Planarity : 0.003 0.032 2085 Dihedral : 8.137 109.582 1764 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.15 % Allowed : 15.85 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (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: -0.92 (0.21), residues: 1440 helix: 1.82 (0.31), residues: 291 sheet: -0.52 (0.30), residues: 312 loop : -1.61 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 409 HIS 0.004 0.001 HIS A 468 PHE 0.013 0.001 PHE A 335 TYR 0.014 0.001 TYR B 187 ARG 0.008 0.000 ARG B 486 *********************** 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 149 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 98 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: C 6 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8094 (pp) REVERT: C 203 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6892 (mm110) REVERT: C 266 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7341 (m-30) REVERT: C 378 LEU cc_start: 0.8298 (mp) cc_final: 0.8081 (tp) REVERT: C 444 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8785 (tp) REVERT: C 493 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6937 (mmm) outliers start: 51 outliers final: 41 residues processed: 135 average time/residue: 0.2274 time to fit residues: 46.0923 Evaluate side-chains 139 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 93 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU 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 170 ILE 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 463 CYS 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 141 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 170 ILE 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 5 CYS Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 37 THR 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 203 GLN Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 282 SER 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 470 CYS 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 136 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 143 optimal weight: 0.0030 chunk 132 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 11 optimal weight: 0.0670 chunk 88 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 overall best weight: 0.4728 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 1.0041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11682 Z= 0.161 Angle : 0.551 8.188 15780 Z= 0.287 Chirality : 0.045 0.390 1728 Planarity : 0.003 0.042 2085 Dihedral : 7.835 107.799 1764 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.09 % Allowed : 16.83 % Favored : 80.08 % 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: -0.68 (0.21), residues: 1440 helix: 2.19 (0.31), residues: 294 sheet: -0.44 (0.30), residues: 312 loop : -1.51 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 409 HIS 0.004 0.001 HIS B 352 PHE 0.012 0.001 PHE A 335 TYR 0.014 0.001 TYR C 364 ARG 0.010 0.000 ARG B 486 ********************** 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 138 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 268 ASN cc_start: 0.7893 (m-40) cc_final: 0.7664 (m-40) REVERT: C 6 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8146 (pp) REVERT: C 266 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7315 (m-30) REVERT: C 444 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8699 (tp) REVERT: C 493 MET cc_start: 0.7284 (mmt) cc_final: 0.7005 (mmm) REVERT: C 494 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7759 (mm-40) outliers start: 38 outliers final: 33 residues processed: 126 average time/residue: 0.2208 time to fit residues: 41.9109 Evaluate side-chains 129 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU 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 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 444 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 170 ILE 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 5 CYS Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 57 LEU 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 264 GLN Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 282 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 388 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.130809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111729 restraints weight = 15932.056| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.40 r_work: 0.3237 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 1.0057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11682 Z= 0.240 Angle : 0.596 9.531 15780 Z= 0.306 Chirality : 0.046 0.373 1728 Planarity : 0.003 0.041 2085 Dihedral : 8.044 107.845 1764 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.58 % Allowed : 16.67 % Favored : 79.76 % 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: -0.70 (0.21), residues: 1440 helix: 2.18 (0.31), residues: 291 sheet: -0.47 (0.30), residues: 312 loop : -1.50 (0.19), residues: 837 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 0.014 0.001 TYR C 364 ARG 0.010 0.000 ARG B 486 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2717.20 seconds wall clock time: 50 minutes 58.63 seconds (3058.63 seconds total)