Starting phenix.real_space_refine on Sun Sep 29 15:36:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdf_31916/09_2024/7vdf_31916_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdf_31916/09_2024/7vdf_31916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdf_31916/09_2024/7vdf_31916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdf_31916/09_2024/7vdf_31916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdf_31916/09_2024/7vdf_31916_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdf_31916/09_2024/7vdf_31916_trim.cif" } resolution = 2.56 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= 0.002 sd= 0.151 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: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 7251 2.51 5 N 2025 2.21 5 O 2316 1.98 5 H 11043 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22692 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7497 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "B" Number of atoms: 7497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7497 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "C" Number of atoms: 7497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7497 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 11.98, per 1000 atoms: 0.53 Number of scatterers: 22692 At special positions: 0 Unit cell: (84.36, 85.88, 144.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 O 2316 8.00 N 2025 7.00 C 7251 6.00 H 11043 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.04 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 285 " " NAG A 602 " - " ASN A 165 " " NAG A 603 " - " ASN A 81 " " NAG B 601 " - " ASN B 285 " " NAG B 602 " - " ASN B 165 " " NAG B 603 " - " ASN B 81 " " NAG C 603 " - " ASN C 285 " " NAG C 604 " - " ASN C 165 " " NAG C 605 " - " ASN C 81 " Time building additional restraints: 6.13 Conformation dependent library (CDL) restraints added in 1.9 seconds 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 34 sheets defined 26.4% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.907A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 367 through 379 removed outlier: 4.202A pdb=" N GLY A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 455 Processing helix chain 'A' and resid 474 through 483 Processing helix chain 'A' and resid 487 through 501 removed outlier: 4.264A pdb=" N TYR A 491 " --> pdb=" O ASP A 487 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASP A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N GLU A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.940A pdb=" N ASP B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N VAL B 78 " --> pdb=" O HIS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 367 through 379 removed outlier: 4.231A pdb=" N GLY B 379 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 455 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 487 through 501 removed outlier: 4.250A pdb=" N TYR B 491 " --> pdb=" O ASP B 487 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASP B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLU B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.853A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 367 through 379 removed outlier: 4.239A pdb=" N GLY C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 455 Processing helix chain 'C' and resid 474 through 483 Processing helix chain 'C' and resid 487 through 501 removed outlier: 4.330A pdb=" N TYR C 491 " --> pdb=" O ASP C 487 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ASP C 493 " --> pdb=" O ASP C 489 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLU C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 366 removed outlier: 3.764A pdb=" N ASN A 357 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR A 351 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.838A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 4.971A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.461A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 136 through 140 Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 removed outlier: 5.493A pdb=" N ARG A 201 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.306A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 12 through 17 removed outlier: 4.590A pdb=" N TYR B 351 " --> pdb=" O ASP B 366 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN B 357 " --> pdb=" O GLY B 360 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 24 through 26 Processing sheet with id=AB6, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'B' and resid 51 through 54 removed outlier: 5.906A pdb=" N ILE B 51 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N CYS B 277 " --> pdb=" O ILE B 51 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 58 through 61 removed outlier: 6.013A pdb=" N PHE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 101 removed outlier: 6.909A pdb=" N ASP B 101 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N TRP B 234 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 100 through 101 removed outlier: 6.909A pdb=" N ASP B 101 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N TRP B 234 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AC4, first strand: chain 'B' and resid 164 through 169 removed outlier: 5.072A pdb=" N ARG B 201 " --> pdb=" O ASN B 248 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 286 through 288 removed outlier: 4.265A pdb=" N CYS B 281 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 360 through 366 removed outlier: 3.781A pdb=" N ASN C 357 " --> pdb=" O GLY C 360 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYR C 351 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AC8, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC9, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AD1, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.000A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 58 through 61 Processing sheet with id=AD3, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.892A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.892A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AD6, first strand: chain 'C' and resid 164 through 169 removed outlier: 5.050A pdb=" N ARG C 201 " --> pdb=" O ASN C 248 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 286 through 287 524 hydrogen bonds defined for protein. 1434 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: 8.85 Time building geometry restraints manager: 7.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 11037 1.04 - 1.24: 1448 1.24 - 1.44: 3768 1.44 - 1.64: 6598 1.64 - 1.84: 78 Bond restraints: 22929 Sorted by residual: bond pdb=" N SER A 9 " pdb=" CA SER A 9 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N SER B 9 " pdb=" CA SER B 9 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 bond pdb=" N SER C 9 " pdb=" CA SER C 9 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.73e+00 bond pdb=" N SER C 9 " pdb=" H SER C 9 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" N SER B 9 " pdb=" H SER B 9 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.23e+00 ... (remaining 22924 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 39585 1.20 - 2.39: 1453 2.39 - 3.59: 111 3.59 - 4.79: 33 4.79 - 5.99: 14 Bond angle restraints: 41196 Sorted by residual: angle pdb=" CA CYS B 14 " pdb=" CB CYS B 14 " pdb=" SG CYS B 14 " ideal model delta sigma weight residual 114.40 120.12 -5.72 2.30e+00 1.89e-01 6.18e+00 angle pdb=" C LYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta sigma weight residual 122.56 119.39 3.17 1.50e+00 4.44e-01 4.47e+00 angle pdb=" C PHE C 392 " pdb=" N HIS C 393 " pdb=" CA HIS C 393 " ideal model delta sigma weight residual 122.93 119.88 3.05 1.45e+00 4.76e-01 4.41e+00 angle pdb=" C LEU B 13 " pdb=" N CYS B 14 " pdb=" CA CYS B 14 " ideal model delta sigma weight residual 122.45 118.79 3.66 1.78e+00 3.16e-01 4.22e+00 angle pdb=" N CYS B 14 " pdb=" CA CYS B 14 " pdb=" C CYS B 14 " ideal model delta sigma weight residual 107.88 110.71 -2.83 1.41e+00 5.03e-01 4.03e+00 ... (remaining 41191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 10310 21.72 - 43.45: 579 43.45 - 65.17: 142 65.17 - 86.89: 39 86.89 - 108.62: 15 Dihedral angle restraints: 11085 sinusoidal: 6192 harmonic: 4893 Sorted by residual: dihedral pdb=" CA CYS C 97 " pdb=" CB CYS C 97 " pdb=" SG CYS C 97 " pdb=" SG CYS C 139 " ideal model delta sinusoidal sigma weight residual 79.00 8.95 70.05 1 2.00e+01 2.50e-03 1.58e+01 dihedral pdb=" CA CYS B 14 " pdb=" C CYS B 14 " pdb=" N LEU B 15 " pdb=" CA LEU B 15 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" O4 BMA B 605 " pdb=" C4 BMA B 605 " pdb=" C5 BMA B 605 " pdb=" O5 BMA B 605 " ideal model delta sinusoidal sigma weight residual -71.29 -179.91 108.62 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 11082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1570 0.061 - 0.121: 211 0.121 - 0.181: 27 0.181 - 0.242: 1 0.242 - 0.302: 3 Chirality restraints: 1812 Sorted by residual: chirality pdb=" C5 BMA A 605 " pdb=" C4 BMA A 605 " pdb=" C6 BMA A 605 " pdb=" O5 BMA A 605 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C5 BMA B 605 " pdb=" C4 BMA B 605 " pdb=" C6 BMA B 605 " pdb=" O5 BMA B 605 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C5 BMA C 602 " pdb=" C4 BMA C 602 " pdb=" C6 BMA C 602 " pdb=" O5 BMA C 602 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1809 not shown) Planarity restraints: 3495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 20 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.47e+00 pdb=" N PRO A 21 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 73 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO A 74 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 283 " -0.017 5.00e-02 4.00e+02 2.59e-02 1.07e+00 pdb=" N PRO B 284 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " -0.015 5.00e-02 4.00e+02 ... (remaining 3492 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 935 2.15 - 2.76: 45082 2.76 - 3.37: 68804 3.37 - 3.99: 94764 3.99 - 4.60: 143378 Nonbonded interactions: 352963 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 27 " pdb=" O ARG B 383 " model vdw 1.537 2.450 nonbonded pdb=" HZ2 LYS A 27 " pdb=" O ARG B 383 " model vdw 1.540 2.450 nonbonded pdb=" OD2 ASP A 415 " pdb=" HZ2 LYS B 391 " model vdw 1.569 2.450 nonbonded pdb=" H MET B 462 " pdb=" O CYS B 466 " model vdw 1.575 2.450 nonbonded pdb=" HZ1 LYS A 391 " pdb=" OD2 ASP C 419 " model vdw 1.583 2.450 ... (remaining 352958 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' and (resid 9 through 501 or resid 601 or resid 603 through 604)) selection = (chain 'B' and (resid 9 through 501 or resid 601 or resid 603 through 604)) selection = (chain 'C' and (resid 9 through 501 or resid 601 or resid 603 through 604)) } 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: 1.610 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: 0.430 Extract box with map and model: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 51.070 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 : 0.004 0.042 11886 Z= 0.234 Angle : 0.548 5.986 16122 Z= 0.275 Chirality : 0.046 0.302 1812 Planarity : 0.003 0.035 2094 Dihedral : 15.734 108.615 4599 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.05 (0.21), residues: 1443 helix: 2.24 (0.26), residues: 339 sheet: -0.79 (0.29), residues: 315 loop : -0.70 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 222 HIS 0.003 0.001 HIS A 393 PHE 0.012 0.001 PHE C 120 TYR 0.007 0.001 TYR C 308 ARG 0.007 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.865 Fit side-chains revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7466 (ttp-110) cc_final: 0.7235 (ttm-80) REVERT: B 450 LYS cc_start: 0.6872 (mtmt) cc_final: 0.6569 (mttt) REVERT: C 57 ARG cc_start: 0.7505 (ttp-110) cc_final: 0.7139 (ttt-90) REVERT: C 493 ASP cc_start: 0.7412 (m-30) cc_final: 0.7147 (m-30) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 2.0707 time to fit residues: 423.3381 Evaluate side-chains 148 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 0.0670 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 overall best weight: 1.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 248 ASN C 173 ASN C 211 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11886 Z= 0.314 Angle : 0.549 8.178 16122 Z= 0.287 Chirality : 0.044 0.179 1812 Planarity : 0.005 0.055 2094 Dihedral : 8.335 57.509 1878 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.63 % Allowed : 5.82 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.23 (0.21), residues: 1443 helix: 1.85 (0.25), residues: 339 sheet: -0.51 (0.33), residues: 261 loop : -0.89 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 127 HIS 0.004 0.001 HIS A 393 PHE 0.012 0.001 PHE C 79 TYR 0.009 0.002 TYR B 351 ARG 0.004 0.000 ARG C 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7473 (ttp-110) cc_final: 0.7244 (ttt-90) REVERT: B 238 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.8022 (mtmm) REVERT: B 450 LYS cc_start: 0.6872 (mtmt) cc_final: 0.6543 (mttp) REVERT: B 493 ASP cc_start: 0.7213 (m-30) cc_final: 0.6824 (m-30) REVERT: C 57 ARG cc_start: 0.7547 (ttp-110) cc_final: 0.7219 (ttt-90) outliers start: 8 outliers final: 6 residues processed: 180 average time/residue: 1.9383 time to fit residues: 388.8514 Evaluate side-chains 165 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 158 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 301 THR 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: 3.9990 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN B 454 GLN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11886 Z= 0.381 Angle : 0.558 9.726 16122 Z= 0.294 Chirality : 0.044 0.150 1812 Planarity : 0.005 0.071 2094 Dihedral : 6.675 57.084 1878 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.10 % Allowed : 8.49 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.52 (0.21), residues: 1443 helix: 1.35 (0.26), residues: 357 sheet: -0.55 (0.32), residues: 267 loop : -1.06 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 421 HIS 0.005 0.001 HIS A 75 PHE 0.012 0.002 PHE B 120 TYR 0.009 0.002 TYR B 351 ARG 0.004 0.000 ARG C 405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7449 (ttp-110) cc_final: 0.7200 (ttt-90) REVERT: B 238 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7921 (mtmm) REVERT: C 57 ARG cc_start: 0.7556 (ttp-110) cc_final: 0.7156 (ttt-90) REVERT: C 375 ASP cc_start: 0.7371 (m-30) cc_final: 0.7140 (m-30) REVERT: C 452 ARG cc_start: 0.7901 (ttm-80) cc_final: 0.7384 (ttm-80) outliers start: 14 outliers final: 6 residues processed: 178 average time/residue: 1.9201 time to fit residues: 382.4818 Evaluate side-chains 163 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 156 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 454 GLN B 33 GLN B 173 ASN B 407 GLN B 454 GLN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11886 Z= 0.263 Angle : 0.512 9.192 16122 Z= 0.269 Chirality : 0.043 0.148 1812 Planarity : 0.004 0.051 2094 Dihedral : 6.058 53.480 1878 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.10 % Allowed : 10.38 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.56 (0.21), residues: 1443 helix: 1.53 (0.26), residues: 354 sheet: -0.76 (0.32), residues: 279 loop : -1.11 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 127 HIS 0.004 0.001 HIS A 393 PHE 0.011 0.001 PHE B 120 TYR 0.008 0.001 TYR B 308 ARG 0.003 0.000 ARG C 405 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7464 (ttp-110) cc_final: 0.7193 (ttt-90) REVERT: B 238 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7879 (mtmm) REVERT: B 312 ASN cc_start: 0.7741 (p0) cc_final: 0.7280 (t0) REVERT: C 57 ARG cc_start: 0.7546 (ttp-110) cc_final: 0.7166 (ttt-90) REVERT: C 375 ASP cc_start: 0.7354 (m-30) cc_final: 0.7124 (m-30) outliers start: 14 outliers final: 6 residues processed: 179 average time/residue: 1.9567 time to fit residues: 394.4881 Evaluate side-chains 162 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 454 GLN B 33 GLN B 173 ASN B 407 GLN B 454 GLN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11886 Z= 0.252 Angle : 0.502 9.039 16122 Z= 0.263 Chirality : 0.043 0.148 1812 Planarity : 0.004 0.047 2094 Dihedral : 5.643 50.333 1878 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.10 % Allowed : 11.79 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.52 (0.21), residues: 1443 helix: 1.84 (0.26), residues: 339 sheet: -0.89 (0.29), residues: 309 loop : -1.10 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 127 HIS 0.004 0.001 HIS A 393 PHE 0.010 0.001 PHE B 120 TYR 0.008 0.001 TYR B 308 ARG 0.004 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 MET cc_start: 0.8346 (ttm) cc_final: 0.7926 (ttm) REVERT: B 57 ARG cc_start: 0.7467 (ttp-110) cc_final: 0.7200 (ttt-90) REVERT: B 238 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7903 (mtmm) REVERT: C 57 ARG cc_start: 0.7546 (ttp-110) cc_final: 0.7156 (ttt-90) REVERT: C 375 ASP cc_start: 0.7363 (m-30) cc_final: 0.7118 (m-30) REVERT: C 452 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7421 (ttm-80) outliers start: 14 outliers final: 8 residues processed: 170 average time/residue: 1.8720 time to fit residues: 356.6719 Evaluate side-chains 166 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 157 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 4.9990 chunk 125 optimal weight: 0.0470 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 454 GLN A 498 ASN B 33 GLN B 173 ASN B 454 GLN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN C 454 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11886 Z= 0.267 Angle : 0.507 9.007 16122 Z= 0.266 Chirality : 0.043 0.147 1812 Planarity : 0.004 0.050 2094 Dihedral : 5.506 47.878 1878 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.10 % Allowed : 12.26 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.52 (0.21), residues: 1443 helix: 1.85 (0.26), residues: 339 sheet: -0.88 (0.29), residues: 309 loop : -1.11 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 127 HIS 0.003 0.001 HIS A 393 PHE 0.010 0.001 PHE B 120 TYR 0.008 0.001 TYR B 308 ARG 0.004 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 166 time to evaluate : 1.786 Fit side-chains revert: symmetry clash REVERT: A 346 MET cc_start: 0.8335 (ttm) cc_final: 0.7908 (ttm) REVERT: B 57 ARG cc_start: 0.7494 (ttp-110) cc_final: 0.7193 (ttt-90) REVERT: C 57 ARG cc_start: 0.7540 (ttp-110) cc_final: 0.7156 (ttt-90) REVERT: C 375 ASP cc_start: 0.7393 (m-30) cc_final: 0.7186 (m-30) outliers start: 14 outliers final: 9 residues processed: 176 average time/residue: 1.8111 time to fit residues: 358.8348 Evaluate side-chains 166 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 157 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN B 33 GLN B 173 ASN B 454 GLN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN C 454 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11886 Z= 0.291 Angle : 0.517 9.292 16122 Z= 0.271 Chirality : 0.043 0.147 1812 Planarity : 0.004 0.054 2094 Dihedral : 5.517 46.797 1878 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.34 % Allowed : 12.97 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.50 (0.21), residues: 1443 helix: 1.80 (0.26), residues: 339 sheet: -0.72 (0.32), residues: 276 loop : -1.13 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 127 HIS 0.003 0.001 HIS A 393 PHE 0.010 0.001 PHE B 120 TYR 0.008 0.001 TYR C 195 ARG 0.005 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 1.768 Fit side-chains REVERT: A 57 ARG cc_start: 0.7345 (ttp-170) cc_final: 0.7059 (ttt-90) REVERT: A 346 MET cc_start: 0.8333 (ttm) cc_final: 0.7902 (ttm) REVERT: B 57 ARG cc_start: 0.7525 (ttp-110) cc_final: 0.7208 (ttt-90) REVERT: B 238 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7918 (mtmm) REVERT: C 375 ASP cc_start: 0.7379 (m-30) cc_final: 0.7163 (m-30) REVERT: C 385 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6829 (mt) outliers start: 17 outliers final: 8 residues processed: 170 average time/residue: 1.7266 time to fit residues: 331.5785 Evaluate side-chains 165 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 155 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 454 GLN B 33 GLN B 173 ASN B 454 GLN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11886 Z= 0.233 Angle : 0.498 8.822 16122 Z= 0.261 Chirality : 0.042 0.148 1812 Planarity : 0.004 0.042 2094 Dihedral : 5.302 44.214 1878 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.94 % Allowed : 13.29 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.48 (0.21), residues: 1443 helix: 1.87 (0.26), residues: 339 sheet: -0.85 (0.30), residues: 306 loop : -1.09 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 127 HIS 0.003 0.001 HIS A 393 PHE 0.010 0.001 PHE B 120 TYR 0.013 0.001 TYR C 195 ARG 0.005 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 1.775 Fit side-chains REVERT: A 57 ARG cc_start: 0.7301 (ttp-170) cc_final: 0.7025 (ttt-90) REVERT: A 346 MET cc_start: 0.8287 (ttm) cc_final: 0.7886 (ttm) REVERT: B 57 ARG cc_start: 0.7544 (ttp-110) cc_final: 0.7223 (ttt-90) REVERT: B 346 MET cc_start: 0.8355 (ttm) cc_final: 0.8035 (ttm) REVERT: C 57 ARG cc_start: 0.7529 (ttp-110) cc_final: 0.7167 (ttt-90) REVERT: C 375 ASP cc_start: 0.7357 (m-30) cc_final: 0.7144 (m-30) REVERT: C 385 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6853 (mt) outliers start: 12 outliers final: 7 residues processed: 170 average time/residue: 1.7698 time to fit residues: 341.4091 Evaluate side-chains 164 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 454 GLN B 33 GLN B 173 ASN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11886 Z= 0.223 Angle : 0.497 8.682 16122 Z= 0.260 Chirality : 0.042 0.148 1812 Planarity : 0.004 0.042 2094 Dihedral : 5.197 43.039 1878 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.71 % Allowed : 14.07 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.46 (0.21), residues: 1443 helix: 1.91 (0.26), residues: 339 sheet: -0.83 (0.30), residues: 306 loop : -1.08 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 127 HIS 0.003 0.001 HIS A 393 PHE 0.010 0.001 PHE B 120 TYR 0.013 0.001 TYR C 195 ARG 0.005 0.000 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.7315 (ttp-170) cc_final: 0.7041 (ttt-90) REVERT: A 346 MET cc_start: 0.8266 (ttm) cc_final: 0.7855 (ttm) REVERT: B 57 ARG cc_start: 0.7555 (ttp-110) cc_final: 0.7223 (ttt-90) REVERT: B 346 MET cc_start: 0.8291 (ttm) cc_final: 0.7950 (ttm) REVERT: C 57 ARG cc_start: 0.7526 (ttp-110) cc_final: 0.7166 (ttt-90) REVERT: C 375 ASP cc_start: 0.7381 (m-30) cc_final: 0.7173 (m-30) REVERT: C 385 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6893 (mt) outliers start: 9 outliers final: 7 residues processed: 165 average time/residue: 1.7528 time to fit residues: 326.7853 Evaluate side-chains 160 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 152 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN B 33 GLN B 173 ASN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11886 Z= 0.386 Angle : 0.577 9.876 16122 Z= 0.302 Chirality : 0.044 0.149 1812 Planarity : 0.005 0.067 2094 Dihedral : 5.704 47.371 1878 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.71 % Allowed : 14.39 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.56 (0.21), residues: 1443 helix: 1.68 (0.26), residues: 339 sheet: -0.79 (0.32), residues: 270 loop : -1.12 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 421 HIS 0.006 0.001 HIS B 75 PHE 0.010 0.002 PHE B 79 TYR 0.014 0.002 TYR C 195 ARG 0.006 0.000 ARG A 261 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 157 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.7379 (ttp-170) cc_final: 0.7088 (ttt-90) REVERT: A 346 MET cc_start: 0.8300 (ttm) cc_final: 0.7881 (ttm) REVERT: A 368 LYS cc_start: 0.7424 (mppt) cc_final: 0.6709 (ttpp) REVERT: B 57 ARG cc_start: 0.7565 (ttp-110) cc_final: 0.7254 (ttt-90) REVERT: C 57 ARG cc_start: 0.7559 (ttp-110) cc_final: 0.7197 (ttt-90) REVERT: C 385 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6886 (mt) outliers start: 9 outliers final: 7 residues processed: 163 average time/residue: 1.8690 time to fit residues: 343.6290 Evaluate side-chains 161 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN A 498 ASN B 173 ASN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN B 454 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.153662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.127883 restraints weight = 34425.338| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.54 r_work: 0.3516 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11886 Z= 0.206 Angle : 0.508 9.706 16122 Z= 0.266 Chirality : 0.043 0.148 1812 Planarity : 0.004 0.041 2094 Dihedral : 5.282 46.253 1878 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.79 % Allowed : 14.31 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.50 (0.21), residues: 1443 helix: 1.86 (0.26), residues: 339 sheet: -0.93 (0.29), residues: 309 loop : -1.06 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 127 HIS 0.003 0.001 HIS A 393 PHE 0.009 0.001 PHE B 120 TYR 0.012 0.001 TYR C 195 ARG 0.006 0.000 ARG A 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7788.67 seconds wall clock time: 135 minutes 39.16 seconds (8139.16 seconds total)