Starting phenix.real_space_refine on Sat Apr 6 04:52:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tcf_41153/04_2024/8tcf_41153.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tcf_41153/04_2024/8tcf_41153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tcf_41153/04_2024/8tcf_41153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tcf_41153/04_2024/8tcf_41153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tcf_41153/04_2024/8tcf_41153.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tcf_41153/04_2024/8tcf_41153.pdb" } resolution = 2.9 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= 0.000 sd= 0.048 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 Mg 1 5.21 5 S 35 5.16 5 C 4443 2.51 5 N 1179 2.21 5 O 1387 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A ASP 148": "OD1" <-> "OD2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7050 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3406 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 21, 'TRANS': 422} Chain: "B" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2823 Classifications: {'peptide': 359} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 341} Chain breaks: 1 Chain: "C" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 603 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 1, ' MG': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.39, per 1000 atoms: 0.62 Number of scatterers: 7050 At special positions: 0 Unit cell: (72.93, 98.736, 107.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 35 16.00 Mg 1 11.99 O 1387 8.00 N 1179 7.00 C 4443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 67 " distance=2.04 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS A 401 " - pdb=" SG CYS B 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 265 " distance=2.02 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 377 " distance=2.09 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 425 " distance=2.02 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 74 " distance=2.04 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 ALPHA1-2 " MAN D 4 " - " MAN D 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A 505 " - " ASN A 260 " " NAG B2003 " - " ASN B 191 " " NAG B2004 " - " ASN B 360 " " NAG B2005 " - " ASN B 379 " " NAG D 1 " - " ASN A 266 " " NAG E 1 " - " ASN A 44 " " NAG F 1 " - " ASN B 389 " " NAG G 1 " - " ASN B 414 " Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1606 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 14 sheets defined 18.5% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 120 through 127 removed outlier: 4.007A pdb=" N SER B 126 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 135 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 191 through 201 Processing helix chain 'B' and resid 213 through 224 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 250 through 256 Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 330 through 343 Processing helix chain 'C' and resid 13 through 29 Processing helix chain 'C' and resid 51 through 63 removed outlier: 4.094A pdb=" N LYS C 55 " --> pdb=" O GLU C 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 4.236A pdb=" N THR A 413 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 424 " --> pdb=" O GLY A 411 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLY A 411 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY A 426 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N MET A 409 " --> pdb=" O GLY A 426 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 7.089A pdb=" N ASP A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.502A pdb=" N HIS A 113 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 101 removed outlier: 3.915A pdb=" N SER A 97 " --> pdb=" O CYS A 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.516A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.618A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 255 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 283 Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 348 removed outlier: 6.297A pdb=" N ILE A 344 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ALA A 361 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ALA A 359 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 348 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 63 through 65 removed outlier: 6.588A pdb=" N VAL B 81 " --> pdb=" O HIS B 420 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N HIS B 422 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE B 83 " --> pdb=" O HIS B 422 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AB4, first strand: chain 'B' and resid 182 through 189 removed outlier: 5.343A pdb=" N HIS B 184 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER B 148 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU B 188 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU B 144 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N TYR B 103 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP B 141 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU B 237 " --> pdb=" O PRO B 104 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 106 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU B 239 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR B 108 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N MET B 241 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU B 110 " --> pdb=" O MET B 241 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ILE B 320 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL B 297 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLY B 322 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE B 299 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 33 through 37 removed outlier: 3.870A pdb=" N ASN C 33 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL C 42 " --> pdb=" O PHE C 9 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N CYS C 3 " --> pdb=" O GLY C 48 " (cutoff:3.500A) 246 hydrogen bonds defined for protein. 624 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: 2.68 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1285 1.32 - 1.45: 1894 1.45 - 1.58: 3952 1.58 - 1.71: 15 1.71 - 1.84: 52 Bond restraints: 7198 Sorted by residual: bond pdb=" CA SER B 382 " pdb=" CB SER B 382 " ideal model delta sigma weight residual 1.527 1.474 0.054 1.49e-02 4.50e+03 1.29e+01 bond pdb=" CG PHE A 1 " pdb=" CD1 PHE A 1 " ideal model delta sigma weight residual 1.384 1.456 -0.072 2.10e-02 2.27e+03 1.17e+01 bond pdb=" CG PHE A 1 " pdb=" CD2 PHE A 1 " ideal model delta sigma weight residual 1.384 1.453 -0.069 2.10e-02 2.27e+03 1.08e+01 bond pdb=" C5 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.413 1.479 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" CG ASP B 209 " pdb=" OD2 ASP B 209 " ideal model delta sigma weight residual 1.249 1.188 0.061 1.90e-02 2.77e+03 1.04e+01 ... (remaining 7193 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.29: 215 106.29 - 113.24: 3750 113.24 - 120.19: 2753 120.19 - 127.14: 2983 127.14 - 134.09: 55 Bond angle restraints: 9756 Sorted by residual: angle pdb=" C ALA A 362 " pdb=" N PRO A 363 " pdb=" CA PRO A 363 " ideal model delta sigma weight residual 119.56 128.08 -8.52 1.02e+00 9.61e-01 6.97e+01 angle pdb=" C ALA A 40 " pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 119.56 127.97 -8.41 1.02e+00 9.61e-01 6.80e+01 angle pdb=" C ALA A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta sigma weight residual 119.56 127.75 -8.19 1.02e+00 9.61e-01 6.45e+01 angle pdb=" C CYS A 401 " pdb=" N PRO A 402 " pdb=" CA PRO A 402 " ideal model delta sigma weight residual 119.66 125.45 -5.79 7.30e-01 1.88e+00 6.28e+01 angle pdb=" C ALA A 109 " pdb=" N PRO A 110 " pdb=" CA PRO A 110 " ideal model delta sigma weight residual 119.56 127.48 -7.92 1.02e+00 9.61e-01 6.02e+01 ... (remaining 9751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.32: 4349 21.32 - 42.63: 104 42.63 - 63.95: 25 63.95 - 85.26: 16 85.26 - 106.58: 8 Dihedral angle restraints: 4502 sinusoidal: 1987 harmonic: 2515 Sorted by residual: dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual 93.00 33.56 59.44 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CD ARG B 378 " pdb=" NE ARG B 378 " pdb=" CZ ARG B 378 " pdb=" NH1 ARG B 378 " ideal model delta sinusoidal sigma weight residual 0.00 51.10 -51.10 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CB CYS B 397 " pdb=" SG CYS B 397 " pdb=" SG CYS B 425 " pdb=" CB CYS B 425 " ideal model delta sinusoidal sigma weight residual -86.00 -124.83 38.83 1 1.00e+01 1.00e-02 2.12e+01 ... (remaining 4499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 771 0.078 - 0.157: 256 0.157 - 0.235: 50 0.235 - 0.313: 15 0.313 - 0.392: 15 Chirality restraints: 1107 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.60e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.51e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-02 2.50e+03 3.87e+01 ... (remaining 1104 not shown) Planarity restraints: 1268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 378 " 0.863 9.50e-02 1.11e+02 3.87e-01 9.09e+01 pdb=" NE ARG B 378 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG B 378 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 378 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 378 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B2005 " 0.079 2.00e-02 2.50e+03 6.51e-02 5.29e+01 pdb=" C7 NAG B2005 " -0.022 2.00e-02 2.50e+03 pdb=" C8 NAG B2005 " 0.060 2.00e-02 2.50e+03 pdb=" N2 NAG B2005 " -0.103 2.00e-02 2.50e+03 pdb=" O7 NAG B2005 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B2003 " 0.071 2.00e-02 2.50e+03 5.86e-02 4.29e+01 pdb=" C7 NAG B2003 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG B2003 " 0.054 2.00e-02 2.50e+03 pdb=" N2 NAG B2003 " -0.094 2.00e-02 2.50e+03 pdb=" O7 NAG B2003 " -0.011 2.00e-02 2.50e+03 ... (remaining 1265 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 29 2.42 - 3.04: 4416 3.04 - 3.66: 10012 3.66 - 4.28: 16815 4.28 - 4.90: 27099 Nonbonded interactions: 58371 Sorted by model distance: nonbonded pdb=" OD1 ASP C 12 " pdb="MG MG B2002 " model vdw 1.804 2.170 nonbonded pdb=" OE2 GLU B 212 " pdb="MG MG B2002 " model vdw 1.809 2.170 nonbonded pdb=" OG SER B 114 " pdb="MG MG B2002 " model vdw 2.033 2.170 nonbonded pdb=" OD1 ASP A 416 " pdb="CA CA A 503 " model vdw 2.093 2.510 nonbonded pdb=" OD1 ASP A 414 " pdb="CA CA A 503 " model vdw 2.097 2.510 ... (remaining 58366 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 'E' selection = chain 'F' selection = chain 'G' } 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 9.330 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.940 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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 : 0.014 0.080 7198 Z= 0.914 Angle : 1.405 8.517 9756 Z= 0.948 Chirality : 0.090 0.392 1107 Planarity : 0.012 0.387 1260 Dihedral : 12.163 106.579 2869 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.68 % Favored : 96.21 % Rotamer: Outliers : 0.41 % Allowed : 0.95 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.27 (0.27), residues: 870 helix: -0.59 (0.43), residues: 119 sheet: 0.85 (0.29), residues: 291 loop : 0.06 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.006 TRP B 230 HIS 0.007 0.001 HIS C 37 PHE 0.024 0.004 PHE A 276 TYR 0.034 0.006 TYR A 112 ARG 0.005 0.001 ARG B 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 178 time to evaluate : 0.800 Fit side-chains REVERT: A 162 ASP cc_start: 0.7276 (t0) cc_final: 0.6964 (t0) outliers start: 3 outliers final: 1 residues processed: 179 average time/residue: 1.2084 time to fit residues: 227.7595 Evaluate side-chains 85 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 381 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN B 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7198 Z= 0.244 Angle : 0.648 9.349 9756 Z= 0.340 Chirality : 0.049 0.195 1107 Planarity : 0.005 0.043 1260 Dihedral : 8.632 83.985 1274 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.87 % Favored : 97.01 % Rotamer: Outliers : 2.98 % Allowed : 11.64 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.47 (0.27), residues: 870 helix: -0.06 (0.46), residues: 126 sheet: 0.85 (0.28), residues: 305 loop : 0.16 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 93 HIS 0.009 0.002 HIS B 118 PHE 0.020 0.002 PHE A 276 TYR 0.021 0.002 TYR A 112 ARG 0.007 0.001 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.796 Fit side-chains REVERT: B 375 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7187 (tm-30) outliers start: 22 outliers final: 9 residues processed: 109 average time/residue: 1.1345 time to fit residues: 131.3712 Evaluate side-chains 88 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 46 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 0.4980 chunk 69 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 206 ASN A 320 GLN B 63 HIS B 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7198 Z= 0.255 Angle : 0.601 5.893 9756 Z= 0.313 Chirality : 0.048 0.261 1107 Planarity : 0.004 0.047 1260 Dihedral : 7.862 72.164 1274 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.64 % Favored : 97.24 % Rotamer: Outliers : 3.79 % Allowed : 12.72 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.47 (0.28), residues: 870 helix: -0.03 (0.46), residues: 128 sheet: 0.90 (0.29), residues: 303 loop : 0.10 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 179 HIS 0.008 0.002 HIS B 63 PHE 0.019 0.002 PHE C 7 TYR 0.016 0.002 TYR A 178 ARG 0.006 0.001 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 81 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: B 193 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8109 (p) REVERT: B 201 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7293 (ttm170) REVERT: B 394 MET cc_start: 0.6258 (tpt) cc_final: 0.5733 (tpt) outliers start: 28 outliers final: 15 residues processed: 101 average time/residue: 1.1117 time to fit residues: 119.3673 Evaluate side-chains 87 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 64 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7198 Z= 0.206 Angle : 0.561 6.313 9756 Z= 0.291 Chirality : 0.047 0.264 1107 Planarity : 0.004 0.048 1260 Dihedral : 7.439 66.323 1274 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.87 % Favored : 97.01 % Rotamer: Outliers : 3.25 % Allowed : 14.07 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.28), residues: 870 helix: -0.17 (0.45), residues: 134 sheet: 1.03 (0.29), residues: 297 loop : -0.02 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 60 HIS 0.006 0.001 HIS C 37 PHE 0.015 0.001 PHE A 276 TYR 0.027 0.002 TYR C 43 ARG 0.006 0.001 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 0.814 Fit side-chains REVERT: B 394 MET cc_start: 0.6292 (tpt) cc_final: 0.5773 (tpt) REVERT: C 71 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6581 (mt-10) outliers start: 24 outliers final: 15 residues processed: 98 average time/residue: 1.0188 time to fit residues: 106.8333 Evaluate side-chains 89 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 43 TYR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 71 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 0.0670 chunk 70 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7198 Z= 0.201 Angle : 0.561 6.180 9756 Z= 0.289 Chirality : 0.047 0.268 1107 Planarity : 0.004 0.049 1260 Dihedral : 7.105 60.747 1274 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.99 % Favored : 96.90 % Rotamer: Outliers : 3.25 % Allowed : 14.34 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.28), residues: 870 helix: -0.10 (0.46), residues: 134 sheet: 1.04 (0.29), residues: 291 loop : -0.07 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.005 0.001 HIS C 37 PHE 0.014 0.001 PHE A 276 TYR 0.035 0.002 TYR C 43 ARG 0.005 0.001 ARG C 6 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 394 MET cc_start: 0.6316 (tpt) cc_final: 0.5810 (tpt) REVERT: B 418 LYS cc_start: 0.7723 (mtpm) cc_final: 0.7514 (mtpm) REVERT: C 13 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7390 (mpp) REVERT: C 71 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6751 (mt-10) outliers start: 24 outliers final: 16 residues processed: 95 average time/residue: 0.9974 time to fit residues: 101.2671 Evaluate side-chains 91 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 71 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 48 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 0.0040 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7198 Z= 0.193 Angle : 0.554 6.248 9756 Z= 0.286 Chirality : 0.047 0.264 1107 Planarity : 0.004 0.046 1260 Dihedral : 6.773 57.286 1273 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.76 % Favored : 97.13 % Rotamer: Outliers : 3.38 % Allowed : 14.88 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.40 (0.28), residues: 870 helix: -0.08 (0.47), residues: 134 sheet: 1.04 (0.29), residues: 291 loop : -0.06 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 179 HIS 0.007 0.001 HIS C 37 PHE 0.024 0.001 PHE B 93 TYR 0.033 0.002 TYR C 43 ARG 0.005 0.001 ARG C 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 79 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: B 394 MET cc_start: 0.6306 (tpt) cc_final: 0.5813 (tpt) outliers start: 25 outliers final: 17 residues processed: 94 average time/residue: 1.0328 time to fit residues: 103.7069 Evaluate side-chains 88 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 68 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.0070 chunk 49 optimal weight: 1.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7198 Z= 0.269 Angle : 0.594 6.783 9756 Z= 0.307 Chirality : 0.049 0.269 1107 Planarity : 0.004 0.052 1260 Dihedral : 6.957 56.043 1273 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.79 % Favored : 96.09 % Rotamer: Outliers : 3.25 % Allowed : 15.43 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.36 (0.29), residues: 870 helix: 0.07 (0.48), residues: 126 sheet: 0.93 (0.29), residues: 289 loop : -0.09 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.007 0.001 HIS C 37 PHE 0.019 0.002 PHE B 93 TYR 0.026 0.002 TYR C 43 ARG 0.006 0.001 ARG C 6 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 74 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: B 394 MET cc_start: 0.6349 (tpt) cc_final: 0.5889 (tpt) REVERT: C 13 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7397 (mpp) outliers start: 24 outliers final: 17 residues processed: 88 average time/residue: 1.0069 time to fit residues: 95.0734 Evaluate side-chains 88 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 46 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 7198 Z= 0.434 Angle : 0.704 9.706 9756 Z= 0.362 Chirality : 0.053 0.272 1107 Planarity : 0.005 0.062 1260 Dihedral : 7.548 58.117 1273 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.14 % Favored : 95.75 % Rotamer: Outliers : 3.25 % Allowed : 15.56 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.14 (0.28), residues: 870 helix: -0.50 (0.45), residues: 133 sheet: 0.80 (0.30), residues: 282 loop : -0.49 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 179 HIS 0.006 0.002 HIS A 91 PHE 0.023 0.002 PHE A 163 TYR 0.032 0.003 TYR C 43 ARG 0.006 0.001 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 76 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 369 LYS cc_start: 0.7702 (mmpt) cc_final: 0.7382 (mtmt) REVERT: B 394 MET cc_start: 0.6427 (tpt) cc_final: 0.5943 (tpt) REVERT: C 13 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7389 (mpp) outliers start: 24 outliers final: 16 residues processed: 92 average time/residue: 1.1117 time to fit residues: 109.2505 Evaluate side-chains 91 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 46 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 0.0570 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7198 Z= 0.219 Angle : 0.591 6.294 9756 Z= 0.306 Chirality : 0.048 0.252 1107 Planarity : 0.004 0.049 1260 Dihedral : 7.067 55.776 1273 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.22 % Favored : 96.67 % Rotamer: Outliers : 2.17 % Allowed : 17.32 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.12 (0.29), residues: 870 helix: 0.06 (0.48), residues: 126 sheet: 0.77 (0.30), residues: 275 loop : -0.27 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 179 HIS 0.007 0.001 HIS C 37 PHE 0.026 0.001 PHE B 93 TYR 0.036 0.002 TYR C 43 ARG 0.005 0.000 ARG C 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 369 LYS cc_start: 0.7623 (mmpt) cc_final: 0.7354 (mtmt) REVERT: B 94 MET cc_start: 0.7603 (tpp) cc_final: 0.7249 (tpt) REVERT: B 394 MET cc_start: 0.6118 (tpt) cc_final: 0.5767 (tpt) REVERT: C 13 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7441 (mpp) REVERT: C 46 VAL cc_start: 0.7981 (OUTLIER) cc_final: 0.7773 (t) outliers start: 16 outliers final: 10 residues processed: 86 average time/residue: 0.9964 time to fit residues: 91.8929 Evaluate side-chains 83 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.0970 chunk 56 optimal weight: 0.9980 chunk 85 optimal weight: 0.1980 chunk 78 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 54 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7198 Z= 0.166 Angle : 0.548 6.016 9756 Z= 0.286 Chirality : 0.047 0.241 1107 Planarity : 0.004 0.039 1260 Dihedral : 6.485 51.214 1273 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.10 % Favored : 96.78 % Rotamer: Outliers : 2.17 % Allowed : 17.46 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.31 (0.29), residues: 870 helix: 0.25 (0.49), residues: 126 sheet: 0.97 (0.30), residues: 278 loop : -0.22 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 114 HIS 0.006 0.001 HIS C 37 PHE 0.026 0.001 PHE B 93 TYR 0.034 0.002 TYR C 43 ARG 0.004 0.000 ARG C 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 369 LYS cc_start: 0.7509 (mmpt) cc_final: 0.7305 (mtmt) REVERT: B 94 MET cc_start: 0.7617 (tpp) cc_final: 0.7254 (tpt) REVERT: B 394 MET cc_start: 0.6047 (tpt) cc_final: 0.5718 (tpt) outliers start: 16 outliers final: 11 residues processed: 89 average time/residue: 1.0558 time to fit residues: 100.4801 Evaluate side-chains 83 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.139981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.113608 restraints weight = 9614.884| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.35 r_work: 0.3424 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7198 Z= 0.207 Angle : 0.574 6.362 9756 Z= 0.299 Chirality : 0.048 0.241 1107 Planarity : 0.004 0.040 1260 Dihedral : 6.504 49.086 1273 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 2.03 % Allowed : 17.19 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.35 (0.29), residues: 870 helix: 0.30 (0.48), residues: 126 sheet: 1.00 (0.31), residues: 278 loop : -0.21 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 114 HIS 0.011 0.001 HIS B 161 PHE 0.028 0.001 PHE B 93 TYR 0.016 0.001 TYR A 178 ARG 0.004 0.000 ARG C 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2765.83 seconds wall clock time: 50 minutes 23.18 seconds (3023.18 seconds total)