Starting phenix.real_space_refine on Sun Feb 18 19:47:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdf_31916/02_2024/7vdf_31916_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdf_31916/02_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_31916/02_2024/7vdf_31916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdf_31916/02_2024/7vdf_31916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdf_31916/02_2024/7vdf_31916_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdf_31916/02_2024/7vdf_31916_trim.pdb" } 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 Residue "A ASP 31": "OD1" <-> "OD2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "C ASP 104": "OD1" <-> "OD2" Residue "C ASP 493": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 10.02, per 1000 atoms: 0.44 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 - 3.50 Amino acid : False - 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: 19.30 Conformation dependent library (CDL) restraints added in 2.5 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: 2.06 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: 9.87 Time building geometry restraints manager: 19.98 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: 100.33 - 107.07: 464 107.07 - 113.80: 27003 113.80 - 120.53: 7121 120.53 - 127.26: 6469 127.26 - 134.00: 139 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 1.850 nonbonded pdb=" HZ2 LYS A 27 " pdb=" O ARG B 383 " model vdw 1.540 1.850 nonbonded pdb=" OD2 ASP A 415 " pdb=" HZ2 LYS B 391 " model vdw 1.569 1.850 nonbonded pdb=" H MET B 462 " pdb=" O CYS B 466 " model vdw 1.575 1.850 nonbonded pdb=" HZ1 LYS A 391 " pdb=" OD2 ASP C 419 " model vdw 1.583 1.850 ... (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 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: 1.450 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: 0.310 Extract box with map and model: 8.020 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 77.230 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.110 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:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.500 ------------------------------------------------------------------------------- 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 : 1.756 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: 2.0861 time to fit residues: 425.2383 Evaluate side-chains 148 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.780 ------------------------------------------------------------------------------- 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: 1.9990 chunk 37 optimal weight: 0.0870 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- 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: 0.7855 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11886 Z= 0.308 Angle : 0.532 8.350 16122 Z= 0.278 Chirality : 0.044 0.174 1812 Planarity : 0.004 0.057 2094 Dihedral : 7.070 58.231 1878 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.55 % Allowed : 5.82 % Favored : 93.63 % 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: -0.11 (0.21), residues: 1443 helix: 2.08 (0.26), residues: 339 sheet: -0.52 (0.33), residues: 261 loop : -0.84 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 127 HIS 0.005 0.001 HIS B 75 PHE 0.012 0.001 PHE C 79 TYR 0.008 0.002 TYR B 351 ARG 0.003 0.000 ARG B 150 *********************** 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 166 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 159 time to evaluate : 1.735 Fit side-chains revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7471 (ttp-110) cc_final: 0.7187 (ttm-80) REVERT: B 450 LYS cc_start: 0.6851 (mtmt) cc_final: 0.6522 (mttp) REVERT: B 493 ASP cc_start: 0.7284 (m-30) cc_final: 0.6912 (m-30) REVERT: C 57 ARG cc_start: 0.7573 (ttp-110) cc_final: 0.7170 (ttt-90) outliers start: 7 outliers final: 6 residues processed: 165 average time/residue: 2.0954 time to fit residues: 384.0524 Evaluate side-chains 158 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 152 time to evaluate : 1.675 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1209 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= 0.392 Angle : 0.556 9.747 16122 Z= 0.291 Chirality : 0.044 0.150 1812 Planarity : 0.005 0.074 2094 Dihedral : 6.295 57.494 1878 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.26 % Allowed : 8.10 % Favored : 90.64 % 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: -0.49 (0.21), residues: 1443 helix: 1.78 (0.26), residues: 342 sheet: -0.75 (0.30), residues: 297 loop : -1.10 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 421 HIS 0.005 0.001 HIS A 75 PHE 0.012 0.002 PHE B 120 TYR 0.008 0.002 TYR B 233 ARG 0.003 0.000 ARG B 150 *********************** 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 183 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 167 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7469 (ttp-110) cc_final: 0.7149 (ttt-90) REVERT: B 238 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7996 (mtmm) REVERT: B 493 ASP cc_start: 0.7242 (m-30) cc_final: 0.6863 (m-30) REVERT: C 57 ARG cc_start: 0.7585 (ttp-110) cc_final: 0.7142 (ttt-90) outliers start: 16 outliers final: 7 residues processed: 174 average time/residue: 2.1377 time to fit residues: 414.6585 Evaluate side-chains 160 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 152 time to evaluate : 1.827 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN B 33 GLN B 173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11886 Z= 0.217 Angle : 0.489 8.658 16122 Z= 0.256 Chirality : 0.042 0.149 1812 Planarity : 0.004 0.045 2094 Dihedral : 5.667 54.044 1878 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.02 % Allowed : 9.83 % Favored : 89.15 % 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: -0.37 (0.21), residues: 1443 helix: 2.00 (0.26), residues: 342 sheet: -1.11 (0.28), residues: 327 loop : -0.86 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 127 HIS 0.003 0.001 HIS A 75 PHE 0.012 0.001 PHE B 120 TYR 0.007 0.001 TYR B 308 ARG 0.003 0.000 ARG C 261 *********************** 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 178 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7479 (ttp-110) cc_final: 0.7162 (ttt-90) REVERT: B 238 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7947 (mtmm) REVERT: C 57 ARG cc_start: 0.7553 (ttp-110) cc_final: 0.7122 (ttt-90) REVERT: C 450 LYS cc_start: 0.7297 (mtpp) cc_final: 0.6134 (mttt) outliers start: 13 outliers final: 7 residues processed: 172 average time/residue: 1.9592 time to fit residues: 375.9647 Evaluate side-chains 164 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 1.792 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN B 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11886 Z= 0.323 Angle : 0.527 9.216 16122 Z= 0.276 Chirality : 0.043 0.146 1812 Planarity : 0.004 0.062 2094 Dihedral : 5.825 56.603 1878 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.86 % Allowed : 10.61 % 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: -0.61 (0.21), residues: 1443 helix: 1.86 (0.26), residues: 342 sheet: -1.00 (0.29), residues: 327 loop : -1.18 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 127 HIS 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE B 120 TYR 0.007 0.002 TYR B 351 ARG 0.003 0.000 ARG B 150 *********************** 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 170 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7456 (ttp-110) cc_final: 0.7107 (ttt-90) REVERT: B 238 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7926 (mtmm) REVERT: C 57 ARG cc_start: 0.7548 (ttp-110) cc_final: 0.7137 (ttt-90) REVERT: C 450 LYS cc_start: 0.7313 (mtpp) cc_final: 0.6191 (mttp) outliers start: 11 outliers final: 8 residues processed: 166 average time/residue: 1.9736 time to fit residues: 366.2855 Evaluate side-chains 160 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 151 time to evaluate : 1.822 ------------------------------------------------------------------------------- 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: 0.6980 chunk 125 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11886 Z= 0.258 Angle : 0.500 8.946 16122 Z= 0.261 Chirality : 0.042 0.147 1812 Planarity : 0.004 0.052 2094 Dihedral : 5.646 56.044 1878 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.18 % Allowed : 11.01 % Favored : 87.81 % 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: -0.42 (0.21), residues: 1443 helix: 1.95 (0.26), residues: 342 sheet: -1.14 (0.29), residues: 327 loop : -0.89 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 127 HIS 0.003 0.001 HIS B 75 PHE 0.011 0.001 PHE B 120 TYR 0.007 0.001 TYR B 308 ARG 0.003 0.000 ARG B 150 *********************** 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 173 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 MET cc_start: 0.8325 (ttm) cc_final: 0.7893 (ttm) REVERT: B 57 ARG cc_start: 0.7468 (ttp-110) cc_final: 0.7102 (ttt-90) REVERT: B 195 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: B 238 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7927 (mtmm) REVERT: C 57 ARG cc_start: 0.7570 (ttp-110) cc_final: 0.7150 (ttt-90) REVERT: C 450 LYS cc_start: 0.7289 (mtpp) cc_final: 0.6171 (mttp) outliers start: 15 outliers final: 8 residues processed: 169 average time/residue: 2.0007 time to fit residues: 383.1834 Evaluate side-chains 166 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 156 time to evaluate : 1.692 ------------------------------------------------------------------------------- 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 195 TYR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN B 33 GLN B 173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11886 Z= 0.326 Angle : 0.531 9.508 16122 Z= 0.277 Chirality : 0.043 0.146 1812 Planarity : 0.005 0.063 2094 Dihedral : 5.863 58.183 1878 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.02 % Allowed : 11.79 % Favored : 87.19 % 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: -0.57 (0.21), residues: 1443 helix: 1.83 (0.26), residues: 342 sheet: -0.88 (0.30), residues: 297 loop : -1.18 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 127 HIS 0.004 0.001 HIS A 75 PHE 0.011 0.002 PHE B 120 TYR 0.010 0.002 TYR C 195 ARG 0.004 0.000 ARG B 150 *********************** 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 170 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 157 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 MET cc_start: 0.8358 (ttm) cc_final: 0.7922 (ttm) REVERT: B 57 ARG cc_start: 0.7471 (ttp-110) cc_final: 0.7124 (ttt-90) REVERT: B 195 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7487 (m-80) REVERT: B 238 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7918 (mtmm) REVERT: C 57 ARG cc_start: 0.7572 (ttp-110) cc_final: 0.7153 (ttt-90) REVERT: C 450 LYS cc_start: 0.7264 (mtpp) cc_final: 0.6181 (mttp) outliers start: 13 outliers final: 7 residues processed: 166 average time/residue: 2.0226 time to fit residues: 374.1795 Evaluate side-chains 162 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 1.806 ------------------------------------------------------------------------------- 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 195 TYR Chi-restraints excluded: chain B residue 238 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11886 Z= 0.241 Angle : 0.497 9.003 16122 Z= 0.260 Chirality : 0.042 0.147 1812 Planarity : 0.004 0.047 2094 Dihedral : 5.636 56.850 1878 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.02 % Allowed : 12.11 % Favored : 86.87 % 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: -0.53 (0.21), residues: 1443 helix: 1.97 (0.26), residues: 342 sheet: -1.01 (0.28), residues: 321 loop : -1.13 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 127 HIS 0.003 0.001 HIS A 75 PHE 0.010 0.001 PHE B 120 TYR 0.009 0.001 TYR C 195 ARG 0.004 0.000 ARG B 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 174 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 MET cc_start: 0.8331 (ttm) cc_final: 0.7899 (ttm) REVERT: B 57 ARG cc_start: 0.7473 (ttp-110) cc_final: 0.7111 (ttt-90) REVERT: B 195 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: B 238 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7961 (mtmm) REVERT: C 57 ARG cc_start: 0.7524 (ttp-110) cc_final: 0.7118 (ttt-90) REVERT: C 450 LYS cc_start: 0.7276 (mtpp) cc_final: 0.6158 (mttp) outliers start: 13 outliers final: 8 residues processed: 169 average time/residue: 1.8672 time to fit residues: 353.8423 Evaluate side-chains 167 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 157 time to evaluate : 1.715 ------------------------------------------------------------------------------- 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 195 TYR 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 65 THR Chi-restraints excluded: chain C residue 195 TYR 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: 0.0980 chunk 121 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1435 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= 0.183 Angle : 0.468 8.075 16122 Z= 0.244 Chirality : 0.042 0.151 1812 Planarity : 0.004 0.040 2094 Dihedral : 5.315 54.443 1878 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.86 % Allowed : 12.50 % 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: -0.39 (0.21), residues: 1443 helix: 2.31 (0.26), residues: 336 sheet: -1.05 (0.27), residues: 339 loop : -1.06 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 127 HIS 0.003 0.001 HIS C 355 PHE 0.009 0.001 PHE B 120 TYR 0.008 0.001 TYR C 195 ARG 0.003 0.000 ARG B 150 *********************** 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 168 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 157 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7411 (ttp-110) cc_final: 0.7051 (ttt-90) REVERT: B 195 TYR cc_start: 0.7829 (OUTLIER) cc_final: 0.7431 (m-80) REVERT: B 238 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8023 (mtmm) REVERT: B 368 LYS cc_start: 0.7272 (mppt) cc_final: 0.6464 (ttpp) REVERT: C 57 ARG cc_start: 0.7511 (ttp-110) cc_final: 0.7097 (ttt-90) REVERT: C 450 LYS cc_start: 0.7238 (mtpp) cc_final: 0.6118 (mttp) outliers start: 11 outliers final: 7 residues processed: 164 average time/residue: 1.8660 time to fit residues: 344.0480 Evaluate side-chains 162 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 1.760 ------------------------------------------------------------------------------- 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 195 TYR Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 195 TYR 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: 3.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 173 ASN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11886 Z= 0.364 Angle : 0.543 9.432 16122 Z= 0.283 Chirality : 0.043 0.146 1812 Planarity : 0.005 0.069 2094 Dihedral : 5.891 59.093 1878 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.86 % Allowed : 12.81 % Favored : 86.32 % 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: -0.54 (0.21), residues: 1443 helix: 1.87 (0.26), residues: 342 sheet: -0.89 (0.30), residues: 297 loop : -1.16 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 234 HIS 0.005 0.001 HIS A 75 PHE 0.010 0.002 PHE B 120 TYR 0.009 0.002 TYR B 351 ARG 0.005 0.000 ARG B 150 ********************** 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 165 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 154 time to evaluate : 1.851 Fit side-chains REVERT: B 57 ARG cc_start: 0.7475 (ttp-110) cc_final: 0.7116 (ttt-90) REVERT: B 195 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.7501 (m-80) REVERT: B 238 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7961 (mtmm) REVERT: B 346 MET cc_start: 0.8352 (ttm) cc_final: 0.8131 (ttm) REVERT: C 57 ARG cc_start: 0.7560 (ttp-110) cc_final: 0.7147 (ttt-90) REVERT: C 450 LYS cc_start: 0.7276 (mtpp) cc_final: 0.6167 (mttp) outliers start: 11 outliers final: 7 residues processed: 162 average time/residue: 1.9330 time to fit residues: 350.6983 Evaluate side-chains 157 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 148 time to evaluate : 1.695 ------------------------------------------------------------------------------- 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 195 TYR Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 195 TYR 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: 8.9990 chunk 105 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.145411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116437 restraints weight = 36222.546| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.70 r_work: 0.3337 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11886 Z= 0.235 Angle : 0.500 9.010 16122 Z= 0.261 Chirality : 0.042 0.148 1812 Planarity : 0.004 0.045 2094 Dihedral : 5.617 56.982 1878 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.94 % Allowed : 12.34 % Favored : 86.71 % 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: -0.26 (0.21), residues: 1443 helix: 2.13 (0.25), residues: 336 sheet: -0.95 (0.31), residues: 291 loop : -0.87 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 127 HIS 0.003 0.001 HIS A 75 PHE 0.010 0.001 PHE B 120 TYR 0.008 0.001 TYR C 195 ARG 0.006 0.000 ARG C 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7878.17 seconds wall clock time: 139 minutes 23.85 seconds (8363.85 seconds total)